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comparison bismark_bowtie2_wrapper.xml @ 0:62c6da72dd4a draft

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date Sat, 06 Jul 2013 09:57:36 -0400
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1 <tool id="bismark_bowtie2" name="Bismark" version="0.7.12">
2 <!-- Wrapper compatible with Bismark version 0.7.11 -->
3 <description>bisulfite mapper (bowtie2)</description>
4 <!--<version_command>bismark version</version_command>-->
5 <requirements>
6 <requirement type="set_environment">SCRIPT_PATH</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement>
8 <requirement type="package" version="2.1.0">bowtie2</requirement>
9 </requirements>
10 <parallelism method="basic"></parallelism>
11 <command interpreter="python">
12 bismark_wrapper.py
13
14 ## Change this to accommodate the number of threads you have available.
15 --num-threads 24
16
17 --bismark_path \$SCRIPT_PATH
18
19 --bowtie2
20
21 ##
22 ## Bismark Genome Preparation, if desired.
23 ##
24
25 ## Handle reference file.
26 #if $refGenomeSource.genomeSource == "history":
27 --own-file=$refGenomeSource.ownFile
28 #else:
29 --indexes-path ${refGenomeSource.index.fields.path}
30 #end if
31
32
33 ##
34 ## Input parameters
35 ##
36
37
38 #if $singlePaired.sPaired == "single":
39 --single-paired $singlePaired.input_singles
40
41 #if $singlePaired.input_singles.ext == "fastqillumina":
42 --phred64-quals
43 --fastq
44 #elif $singlePaired.input_singles.ext == "fastqsanger":
45 --fastq
46 #elif $singlePaired.input_singles.ext == "fasta":
47 --fasta
48 #end if
49 #else:
50 --mate-paired
51 #set $mate1 = list()
52 #set $mate2 = list()
53 #for $mate_pair in $singlePaired.mate_list
54 $mate1.append( str($mate_pair.input_mate1) )
55 $mate2.append( str($mate_pair.input_mate2) )
56 #end for
57
58 --mate1 #echo ','.join($mate1)
59 --mate2 #echo ','.join($mate2)
60
61 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
62 --phred64-quals
63 --fastq
64 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
65 --fastq
66 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
67 --fasta
68 #end if
69
70 -I $singlePaired.minInsert
71 -X $singlePaired.maxInsert
72 #end if
73
74
75 ## for now hardcode the value for the required memory per thread in --best mode
76 --chunkmbs 512
77
78
79 #if $params.settingsType == "custom":
80
81 ## default 20
82 --seed-len $params.seed_len
83 ## default 0
84 --seed-mismatches $params.seed_mismatches
85 ## default 15
86 --seed-extention-attempts $params.seed_extention_attempts
87 ## default 2
88 --max-reseed $params.max_reseed
89
90 ## default 70
91 ##--maqerr $params.maqerr
92
93 ## default unlimited
94 #if $params.qupto != 0:
95 --qupto $params.qupto
96 #end if
97 #if $params.skip_reads != 0:
98 --skip-reads $params.skip_reads
99 #end if
100
101 ## if set, disable the original behaviour
102 $params.no_mixed
103 ## if set, disable the original behaviour
104 $params.no_discordant
105
106 #if $params.bismark_stdout:
107 --stdout $output_stdout
108 #end if
109
110 #if $params.isReportOutput:
111 --output-report-file $report_file
112 #end if
113
114 #end if
115
116 ##
117 ## Output parameters.
118 ##
119 --output $output
120 ##$suppress_header
121
122 #if str( $singlePaired.sPaired ) == "single"
123 #if $output_unmapped_reads_l
124 --output-unmapped-reads $output_unmapped_reads_l
125 #end if
126 #if $output_suppressed_reads_l
127 --output-suppressed-reads $output_suppressed_reads_l
128 #end if
129 #else
130 #if $output_unmapped_reads_l and $output_unmapped_reads_r
131 --output-unmapped-reads-l $output_unmapped_reads_l
132 --output-unmapped-reads-r $output_unmapped_reads_r
133 #end if
134 #if $output_suppressed_reads_l and $output_suppressed_reads_l
135 --output-suppressed-reads-l $output_suppressed_reads_l
136 --output-suppressed-reads-r $output_suppressed_reads_r
137 #end if
138 #end if
139
140 </command>
141 <inputs>
142 <conditional name="refGenomeSource">
143 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
144 <option value="indexed">Use a built-in index</option>
145 <option value="history">Use one from the history</option>
146 </param>
147 <when value="indexed">
148 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
149 <options from_data_table="bowtie2_indexes">
150 <filter type="sort_by" column="2"/>
151 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
152 </options>
153 </param>
154 </when> <!-- build-in -->
155 <when value="history">
156 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
157 </when> <!-- history -->
158 </conditional> <!-- refGenomeSource -->
159
160 <!-- Input Parameters -->
161 <conditional name="singlePaired">
162 <param name="sPaired" type="select" label="Is this library mate-paired?">
163 <option value="single">Single-end</option>
164 <option value="paired">Paired-end</option>
165 </param>
166 <when value="single">
167 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
168 </when>
169 <when value="paired">
170 <repeat name="mate_list" title="Paired End Pairs" min="1">
171 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
172 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
173 </repeat>
174 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
175 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
176 </when>
177 </conditional>
178
179
180 <conditional name="params">
181 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
182 <option value="default">Use Defaults</option>
183 <option value="custom">Full parameter list</option>
184 </param>
185 <when value="default" />
186 <!-- Full/advanced params. -->
187 <when value="custom">
188 <!-- -N -->
189 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
190 <!-- -L -->
191 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
192 <!--
193 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
194 -->
195 <!-- -D -->
196 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
197 <!-- -R -->
198 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
199
200 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
201 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
202
203 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
204 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
205
206 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
207 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" />
208 <!-- output Options -->
209 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
210 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
211
212 <!--end output options -->
213 </when> <!-- full -->
214 </conditional> <!-- params -->
215 <!--
216 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" checked="false" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default." />
217 -->
218 </inputs>
219
220
221 <outputs>
222 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
223 <filter>
224 ((
225 params['settingsType'] == "custom" and
226 params['isReportOutput'] is True
227 ))
228 </filter>
229 </data>
230 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
231 <filter>
232 ((
233 params['settingsType'] == "custom" and
234 params['bismark_stdout'] is True
235 ))
236 </filter>
237 </data>
238
239 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
240 <actions>
241 <conditional name="refGenomeSource.genomeSource">
242 <when value="indexed">
243 <action type="metadata" name="dbkey">
244 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
245 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
246 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
247 </option>
248 </action>
249 </when>
250 <when value="history">
251 <action type="metadata" name="dbkey">
252 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
253 </action>
254 </when>
255 </conditional>
256 </actions>
257 </data>
258
259 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
260 <filter>
261 ((
262 params['settingsType'] == "custom" and
263 params['suppressed_read_file'] is True
264 ))
265 </filter>
266 <actions>
267 <conditional name="singlePaired.sPaired">
268 <when value="single">
269 <action type="format">
270 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
271 </action>
272 </when>
273 <when value="paired">
274 <action type="format">
275 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
276 </action>
277 </when>
278 </conditional>
279 </actions>
280 </data>
281
282 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
283 <filter>singlePaired['sPaired'] == "paired"</filter>
284 <filter>params['settingsType'] == "custom"</filter>
285 <filter>params['supressed_read_file'] is True</filter>
286 <actions>
287 <conditional name="singlePaired.sPaired">
288 <when value="single">
289 <action type="format">
290 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
291 </action>
292 </when>
293 <when value="paired">
294 <action type="format">
295 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
296 </action>
297 </when>
298 </conditional>
299 </actions>
300 </data>
301
302 <!-- Outout unmapped reads -->
303 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
304 <filter>
305 ((
306 params['settingsType'] == "custom" and
307 params['unmapped_read_file'] is True
308 ))
309 </filter>
310 <actions>
311 <conditional name="singlePaired.sPaired">
312 <when value="single">
313 <action type="format">
314 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
315 </action>
316 </when>
317 <when value="paired">
318 <action type="format">
319 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
320 </action>
321 </when>
322 </conditional>
323 </actions>
324 </data>
325
326 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
327 <filter>singlePaired['sPaired'] == "paired"</filter>
328 <filter>params['settingsType'] == "custom"</filter>
329 <filter>params['unmapped_read_file'] is True</filter>
330 <actions>
331 <conditional name="singlePaired.sPaired">
332 <when value="single">
333 <action type="format">
334 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
335 </action>
336 </when>
337 <when value="paired">
338 <action type="format">
339 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
340 </action>
341 </when>
342 </conditional>
343 </actions>
344 </data>
345
346
347 </outputs>
348
349 <tests>
350 </tests>
351
352 <help>
353
354 **What it does**
355
356 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
357 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
358 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
359 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
360 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
361 forward strand, by doing this alignments will produce the same positions). These instances of Bowtie 2
362 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
363 sequence from the genome and determine if there were any protected C's present or not.
364
365 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
366
367 As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
368 re-enabled by using non_directional mode.
369
370 It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
371
372 ------
373
374 **Know what you are doing**
375
376 .. class:: warningmark
377
378 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
379
380 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
381
382
383 .. class:: warningmark
384
385 Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
386
387 ------
388
389 **Input formats**
390
391 Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
392
393 ------
394
395 **A Note on Built-in Reference Genomes**
396
397 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
398
399 ------
400
401 The final output of Bismark is in SAM format by default.
402
403 **Outputs**
404
405 The output is in SAM format, and has the following columns::
406
407 Column Description
408 -------- --------------------------------------------------------
409 1 QNAME seq-ID
410 2 FLAG this flag tries to take the strand a bisulfite read
411 originated from into account
412 (this is different from ordinary DNA alignment flags!)
413 3 RNAME chromosome
414 4 POS start position
415 5 MAPQ always 255
416 6 CIGAR extended CIGAR string
417 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
418 8 MPOS 1-based Mate POSition
419 9 ISIZE Inferred insert SIZE
420 10 SEQ query SEQuence on the same strand as the reference
421 11 QUAL Phred33 scale
422 12 NM-tag edit distance to the reference)
423 13 XX-tag base-by-base mismatches to the reference.
424 This does not include indels.
425 14 XM-tag methylation call string
426 15 XR-tag read conversion state for the alignment
427 16 XG-tag genome conversion state for the alignment
428
429
430 Each read of paired-end alignments is written out in a separate line in the above format.
431
432
433 It looks like this (scroll sideways to see the entire example)::
434
435 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
436 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
437 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
438
439 -------
440
441 **Bismark settings**
442
443 All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
444
445 ------
446
447 **Bismark parameter list**
448
449 This is an exhaustive list of Bismark options.
450
451 Input::
452
453 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
454 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
455 produce one mapping result and one report file per input file.
456
457 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
458 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
459 correspond file-for-file and read-for-read with those specified in mates2.
460 Reads may be a mix of different lengths. Bismark will produce one mapping result
461 and one report file per paired-end input file pair.
462
463 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
464 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
465 correspond file-for-file and read-for-read with those specified in mates1.
466 Reads may be a mix of different lengths.
467
468 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
469 files (usually having extension .fg or .fastq). This is the default. See also
470 --solexa-quals.
471
472 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
473 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
474 are assumed to be 40 on the Phred scale.
475
476 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
477
478 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
479
480 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
481
482 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
483
484 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
485 (which can't). The formula for conversion is:
486 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
487 is usually the right option for use with (unconverted) reads emitted by the GA
488 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
489
490 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
491 reads emitted by GA Pipeline version 1.3 or later. Default: off.
492
493
494 Alignment::
495
496 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
497 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
498 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
499
500 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
501 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
502 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
503
504 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
505 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
506 quality values to the nearest 10 and saturates at 30. This value is not relevant for
507 Bowtie 2.
508
509 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
510 --best mode. Best-first search must keep track of many paths at once to ensure it is
511 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
512 memory impact of the descriptors, but they can still grow very large in some cases. If
513 you receive an error message saying that chunk memory has been exhausted in --best mode,
514 try adjusting this parameter up to dedicate more memory to the descriptors. This value
515 is not relevant for Bowtie 2. Default: 512.
516
517 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
518 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
519 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
520 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
521
522 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
523 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
524 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
525 A 61-bp gap would not be valid in that case. Default: 500.
526
527
528
529 Output::
530
531 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
532 bisulfite strands will be reported. Default: OFF.
533
534 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
535 to the original strands are merely theoretical and should not exist in reality. Specifying directional
536 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
537 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
538 for sprand-specific libraries).
539
540 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
541 split up into several smaller files to run concurrently and the output files are to be merged.
542
543 --quiet Print nothing besides alignments.
544
545 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
546 of SAM format output.
547
548 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
549 appear as they did in the input, without any translation of quality values that may have
550 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
551 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
552 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
553 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
554
555 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
556 mismatches or other reads that fail to align uniquely to a file in the output directory.
557 Written reads will appear as they did in the input, without any of the translation of quality
558 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
559 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
560 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
561
562 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
563 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
564 to create it first. The path to the output folder can be either relative or absolute.
565
566 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
567 the specified folder does not exist, Bismark will attempt to create it first. The path to the
568 temporary folder can be either relative or absolute.
569
570 ------
571
572 Bowtie 2 alignment options::
573
574 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
575 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
576 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
577 Bowtie 1 see -n).
578
579 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
580 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
581 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
582 Bowtie 1 see -l).
583
584 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
585 position to be the highest possible, regardless of the actual value. I.e. input is treated
586 as though all quality values are high. This is also the default behavior when the input
587 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
588
589
590 Bowtie 2 paired-end options::
591
592 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
593 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
594 and on by default.
595
596 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
597 A discordant alignment is an alignment where both mates align uniquely, but that does not
598 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
599 and it is on by default.
600
601
602 Bowtie 2 effort options::
603
604 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
605 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
606 new second-best alignment. Default: 15.
607
608 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
609 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
610 mismatches allowed) at different offsets and searches for more alignments. A read is considered
611 to have repetitive seeds if the total number of seed hits divided by the number of seeds
612 that aligned at least once is greater than 300. Default: 2.
613
614
615 Bowtie 2 Scoring options::
616
617 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
618 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
619 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
620 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
621 L,0,-0.2.
622
623
624 Bowtie 2 Reporting options::
625
626 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
627 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
628 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
629 effort expended to find valid alignments.
630
631 For reference, this used to be the old (now deprecated) description of -M:
632 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
633 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
634 happens first. Only the best alignment is reported. Information from the other alignments is used to
635 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
636 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
637 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
638 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
639 always used and its default value is set to 10.
640
641 </help>
642 </tool>