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comparison bismark_bowtie2_wrapper.xml @ 8:9bfe38410155 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author bgruening
date Wed, 22 Aug 2018 08:09:42 -0400
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7:fcadce4d9a06 8:9bfe38410155
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0" profile="18.01">
2 <description>Bisulfite reads mapper</description>
3 <requirements>
4 <requirement type="package" version="0.20.0">bismark</requirement>
5 <requirement type="package" version="1.8">samtools</requirement>
6 <requirement type="package" version="2.3.4.2">bowtie2</requirement>
7 </requirements>
8 <command><![CDATA[
9 python '$__tool_directory__/bismark_wrapper.py'
10
11 ## Change this to accommodate the number of threads you have available.
12 --num-threads "\${GALAXY_SLOTS:-4}"
13
14 ##
15 ## Bismark Genome Preparation, if desired.
16 ##
17
18 ## Handle reference file.
19 #if $refGenomeSource.genomeSource == "built_in_fasta":
20 --own-file '${refGenomeSource.built_in_fasta.fields.path}'
21 #else if $refGenomeSource.genomeSource == "history":
22 --own-file '$refGenomeSource["own_file"]'
23 #else:
24 --indexes-path '${refGenomeSource.built_in_indexes.fields.path}'
25 #end if
26
27 ##
28 ## Input parameters
29 ##
30
31 #if $singlePaired.sPaired == "single":
32 --single-paired '$singlePaired.input_singles'
33
34 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]:
35 --phred64-quals
36 --fastq
37 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]:
38 --fastq
39 #elif $singlePaired.input_singles.ext == "fasta":
40 --fasta
41 #end if
42 #else:
43 --mate-paired
44 #set $mate1 = list()
45 #set $mate2 = list()
46 #for $mate_pair in $singlePaired.mate_list
47 $mate1.append( str($mate_pair.input_mate1) )
48 $mate2.append( str($mate_pair.input_mate2) )
49 #end for
50
51 --mate1 #echo ','.join($mate1)
52 --mate2 #echo ','.join($mate2)
53
54 #for $mate_pair in $singlePaired.mate_list:
55 #if $mate_pair.input_mate1.ext == "fastqillumina":
56 --phred64-quals
57 --fastq
58 #elif $mate_pair.input_mate1.ext in "fastqsanger,fastqsanger.gz":
59 --fastq
60 #elif $mate_pair.input_mate1.ext == "fasta":
61 --fasta
62 #end if
63 #break
64 #end for
65
66 -I $singlePaired.minInsert
67 -X $singlePaired.maxInsert
68 #end if
69
70 #if $sort_bam:
71 --sort-bam
72 #end if
73
74 ## for now hardcode the value for the required memory per thread in --best mode
75 --chunkmbs 512
76
77
78 #if $params.settingsType == "custom":
79
80 ## default 20
81 --seed-len $params.seed_len
82 ## default 0
83 --seed-mismatches $params.seed_mismatches
84 ## default 15
85 --seed-extention-attempts $params.seed_extention_attempts
86 ## default 2
87 --max-reseed $params.max_reseed
88
89 ## default 70
90 ##--maqerr $params.maqerr
91
92 ## default unlimited
93 #if $params.qupto != 0:
94 --qupto $params.qupto
95 #end if
96 #if $params.skip_reads != 0:
97 --skip-reads $params.skip_reads
98 #end if
99
100 ## if set, disable the original behaviour
101 $params.no_mixed
102 ## if set, disable the original behaviour
103 $params.no_discordant
104
105 #if $params.bismark_stdout:
106 --stdout '$output_stdout'
107 #end if
108
109 #if $params.isReportOutput:
110 --output-report-file '$report_file'
111 #end if
112
113 #else:
114 --output-report-file '$report_file'
115 #end if
116
117 ##
118 ## Output parameters.
119 ##
120 --output '$output'
121 ##$suppress_header
122
123 #if str( $singlePaired.sPaired ) == "single"
124 #if $output_unmapped_reads_l
125 --output-unmapped-reads '$output_unmapped_reads_l'
126 #end if
127 #if $output_suppressed_reads_l
128 --output-suppressed-reads '$output_suppressed_reads_l'
129 #end if
130 #else
131 #if $output_unmapped_reads_l and $output_unmapped_reads_r
132 --output-unmapped-reads-l '$output_unmapped_reads_l'
133 --output-unmapped-reads-r '$output_unmapped_reads_r'
134 #end if
135 #if $output_suppressed_reads_l and $output_suppressed_reads_l
136 --output-suppressed-reads-l '$output_suppressed_reads_l'
137 --output-suppressed-reads-r '$output_suppressed_reads_r'
138 #end if
139 #end if
140
141 ]]>
142 </command>
143 <inputs>
144 <conditional name="refGenomeSource">
145 <param name="genomeSource" type="select"
146 label="Will you select a reference genome from your history or use a built-in index?"
147 help="Built-ins were indexed using default options">
148 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
149 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
150 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
151 </param>
152 <when value="built_in_indexes">
153 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)"
154 help="If your genome of interest is not listed, contact your Galaxy admin">
155 <options from_data_table="bismark_indexes">
156 <filter type="sort_by" column="name"/>
157 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
158 </options>
159 </param>
160 </when>
161 <when value="built_in_fasta">
162 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
163 <options from_data_table="all_fasta">
164 <filter type="sort_by" column="name"/>
165 <validator type="no_options"
166 message="No genomes in fasta are available for the selected input dataset"/>
167 </options>
168 </param>
169 </when>
170 <when value="history">
171 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
172 </when>
173 </conditional>
174
175 <!-- Input Parameters -->
176 <conditional name="singlePaired">
177 <param name="sPaired" type="select" label="Is this library mate-paired?">
178 <option value="single">Single-end</option>
179 <option value="paired">Paired-end</option>
180 </param>
181 <when value="single">
182 <param name="input_singles" type="data"
183 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file"
184 help="FASTQ or FASTA files."/>
185 </when>
186 <when value="paired">
187 <repeat name="mate_list" title="Paired End Pairs" min="1">
188 <param name="input_mate1" type="data"
189 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1"
190 help="FASTQ or FASTA files."/>
191 <param name="input_mate2" type="data"
192 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2"
193 help="FASTQ or FASTA files."/>
194 </repeat>
195 <param name="minInsert" type="integer" value="0"
196 label="Minimum insert size for valid paired-end alignments"/>
197 <param name="maxInsert" type="integer" value="500"
198 label="Maximum insert size for valid paired-end alignments"/>
199 </when>
200 </conditional>
201
202 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False"
203 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
204
205 <conditional name="params">
206 <param name="settingsType" type="select" label="Bismark settings to use"
207 help="You can use the default settings or set custom values for any of Bismark's parameters.">
208 <option value="default">Use Defaults</option>
209 <option value="custom">Full parameter list</option>
210 </param>
211 <!-- Full/advanced params. -->
212 <when value="dafault"></when>
213 <when value="custom">
214 <!-- -N -->
215 <param name="seed_mismatches" type="integer" value="0"
216 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
217 <!-- -L -->
218 <param name="seed_len" type="integer" value="20"
219 label="Length of the seed substrings to align during multiseed alignment"/>
220 <!--
221 <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'." />
222 -->
223 <!-- -D -->
224 <param name="seed_extention_attempts" type="integer" value="15"
225 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
226 <!-- -R -->
227 <param name="max_reseed" type="integer" value="2"
228 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/>
229
230 <param name="qupto" type="integer" value="0"
231 label="Only aligns the first N reads or read pairs from the input"
232 help="Default is 0 and means 'no-limit'."/>
233 <param name="skip_reads" type="integer" value="0"
234 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
235
236 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
237 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
238 help=""/>
239 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
240 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads"
241 help=""/>
242
243 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
244 label="Write ambiguous reads to an extra output file"
245 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."/>
246 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
247 label="Write all reads that could not be aligned to a file"/>
248 <!-- output Options -->
249 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
250 label="Write the bismark output and summary information to an extra file"/>
251 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
252 label="Offer all report files concatenated in one file (Mapping Report)"/>
253
254 <!--end output options -->
255 </when> <!-- full -->
256 </conditional> <!-- params -->
257 <!--
258 <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." />
259 -->
260 </inputs>
261
262
263 <outputs>
264 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
265 <filter>
266 ((
267 params['settingsType'] == "default" or
268 ( params['settingsType'] == "custom" and
269 params['isReportOutput'] is True )
270 ))
271 </filter>
272 </data>
273 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
274 <filter>
275 ((
276 params['settingsType'] == "custom" and
277 params['bismark_stdout'] is True
278 ))
279 </filter>
280 </data>
281
282 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
283 <actions>
284 <conditional name="refGenomeSource.genomeSource">
285 <when value="built_in_indexes">
286 <action type="metadata" name="dbkey">
287 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
288 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
289 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
290 </option>
291 </action>
292 </when>
293 <when value="generate_indexes">
294 <action type="metadata" name="dbkey">
295 <option type="from_data_table" name="all_fasta" column="1" offset="0">
296 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
297 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
298 </option>
299 </action>
300 </when>
301 </conditional>
302 </actions>
303 <change_format>
304 <when input="sort_bam" value="true" format="bam"/>
305 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/>
306 </change_format>
307 </data>
308
309 <data format="fastq" name="output_suppressed_reads_l"
310 label="${tool.name} on ${on_string}: suppressed reads (L)">
311 <filter>
312 ((
313 params['settingsType'] == "custom" and
314 params['suppressed_read_file'] is True
315 ))
316 </filter>
317 <actions>
318 <conditional name="singlePaired.sPaired">
319 <when value="single">
320 <action type="format">
321 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
322 </action>
323 </when>
324 </conditional>
325 </actions>
326 </data>
327
328 <data format="fastq" name="output_suppressed_reads_r"
329 label="${tool.name} on ${on_string}: suppressed reads (R)">
330 <filter>
331 ((
332 singlePaired['sPaired'] == "paired" and
333 params['settingsType'] == "custom" and
334 params['suppressed_read_file'] is True
335 ))
336 </filter>
337 <actions>
338 <conditional name="singlePaired.sPaired">
339 <when value="single">
340 <action type="format">
341 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
342 </action>
343 </when>
344 <!--when value="paired">
345 <action type="format">
346 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
347 </action>
348 </when-->
349 </conditional>
350 </actions>
351 </data>
352
353 <!-- Outout unmapped reads -->
354 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
355 <filter>
356 ((
357 params['settingsType'] == "custom" and
358 params['unmapped_read_file'] is True
359 ))
360 </filter>
361 <actions>
362 <conditional name="singlePaired.sPaired">
363 <when value="single">
364 <action type="format">
365 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
366 </action>
367 </when>
368 <!--when value="paired">
369 <action type="format">
370 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
371 </action>
372 </when-->
373 </conditional>
374 </actions>
375 </data>
376 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
377 <filter>
378 ((
379 singlePaired['sPaired'] == "paired" and
380 params['settingsType'] == "custom" and
381 params['unmapped_read_file'] is True
382 ))
383 </filter>
384 <actions>
385 <conditional name="singlePaired.sPaired">
386 <when value="single">
387 <action type="format">
388 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
389 </action>
390 </when>
391 <!--when value="paired">
392 <action type="format">
393 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
394 </action>
395 </when-->
396 </conditional>
397 </actions>
398 </data>
399 </outputs>
400 <tests>
401 <test>
402 <param name="genomeSource" value="history"/>
403 <param name="own_file" value="mm10.tiny.fa.gz" />
404 <param name="sPaired" value="single"/>
405 <param name="input_singles" value="input1.fq.gz" ftype="fastqsanger"/>
406 <param name="sort_bam" value="false"/>
407 <param name="settingsType" value="custom"/>
408 <param name="suppressed_read_file" value="true"/>
409 <param name="unmapped_read_file" value="true"/>
410 <param name="bismark_stdout" value="true"/>
411 <param name="isReportOutput" value="true"/>
412
413 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80">
414 <assert_contents>
415 <has_text text="Sequences analysed in total:" />
416 <has_text text="44115" />
417 <has_text text="Mapping efficiency:" />
418 <has_text text="1.3%" />
419 <has_text text="Bismark run complete" />
420 </assert_contents>
421 </output>
422 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
423 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
424 </test>
425 </tests>
426
427 <help>
428 <![CDATA[
429
430 **What it does**
431
432 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome.
433 | Sequence reads are transformed into a bisulfite converted forward strand version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
434 | Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the forward strand, by doing this alignments will produce the same positions).
435 | These instances of Bowtie 2 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original sequence from the genome and determine if there were any protected C's present or not.
436 |
437 | 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 re-enabled by using non_directional mode.
438 |
439 | 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.
440
441 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
442
443 ----
444
445 **Know what you are doing**
446
447 .. class:: warningmark
448
449 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco.
450 | In other words = running this tool with default parameters will probably not give you meaningful results.
451 | A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
452 |
453
454 .. class:: warningmark
455
456 | 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.
457
458 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
459
460 ----
461
462 **Input formats**
463
464 | 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.
465
466 ----
467
468 **A Note on Built-in Reference Genomes**
469
470 | 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.
471 | 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.
472 | 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.
473
474 ----
475
476 **Outputs**
477
478 * The final output of Bismark is in SAM format by default, and has the following columns::
479
480 Column Description
481 -------- --------------------------------------------------------
482 1 QNAME seq-ID
483 2 FLAG this flag tries to take the strand a bisulfite read
484 originated from into account
485 (this is different from ordinary DNA alignment flags!)
486 3 RNAME chromosome
487 4 POS start position
488 5 MAPQ always 255
489 6 CIGAR extended CIGAR string
490 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
491 8 MPOS 1-based Mate POSition
492 9 ISIZE Inferred insert SIZE
493 10 SEQ query SEQuence on the same strand as the reference
494 11 QUAL Phred33 scale
495 12 NM-tag edit distance to the reference)
496 13 XX-tag base-by-base mismatches to the reference.
497 This does not include indels.
498 14 XM-tag methylation call string
499 15 XR-tag read conversion state for the alignment
500 16 XG-tag genome conversion state for the alignment
501
502
503 | Each read of paired-end alignments is written out in a separate line in the above format.
504 |
505
506 * It looks like this (scroll sideways to see the entire example)::
507
508 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
509 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
510 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
511
512 ----
513
514 **Note on Bismark settings**
515
516 | 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.
517
518 ----
519
520 **Bismark settings**
521
522 * **If Paired-End Reads**
523
524 * **Minimum insert size for valid paired-end alignments**
525
526 | The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. Default: 0.
527 |
528 | Alignment option *-I/--minins <INT>*
529
530
531 * **Maximum insert size for valid paired-end alignments**
532
533 | The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. Default: 500.
534 |
535 | Alignment option *-X/--maxins <INT>*
536
537
538 * **Number of mismatches to be allowed in a seed alignment during multiseed alignment**
539
540 | Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for Bowtie 1 see -n).
541 |
542 | Bowtie 2 Specific option *-N <INT>*
543
544 * **Length of the seed substrings to align during multiseed alignment**
545
546 | Sets the length of the seed substrings to align during multiseed alignment. Smaller values make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is used by default, which sets -L to 20. This option is only available for Bowtie 2 (for Bowtie 1 see -l).
547 |
548 | Bowtie 2 Specific option *-L <INT>*
549
550
551 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on**
552
553 | Up to <int> consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using the alignments found so far. A seed extension "fails" if it does not yield a new best or a new second-best alignment. Default: 15.
554 |
555 | Bowtie 2 Effort option *-D <INT>*
556
557 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
558
559 | <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default: 2.
560 |
561 | Bowtie 2 Effort option *-R <INT>*
562
563 * **Only aligns the first N reads or read pairs from the input**
564
565 | Only aligns the first <int> reads or read pairs from the input. Default: no limit.
566 |
567 | Input option *-u/--upto <INT>*
568
569 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
570
571 | Input option *-s/--skip*
572
573 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
574
575 | Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior and it is on by default.
576 |
577 | Bowtie 2 Paired-End option *--no-discordant*
578
579 * **Disable Bowtie 2's behaviour to try to find alignments for the individual mates**
580
581 | This option disables Bowtie 2's behavior to try to find alignments for the individual mates if it cannot find a concordant or discordant alignment for a pair. This option is invariable and on by default.
582 |
583 | Bowtie 2 Paired-End option *--no-mixed*
584
585 * **Write ambiguous reads to an extra output file**
586
587 | 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 to a file in the output directory. Written reads will appear as they did in the input, without any of the translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
588 |
589 | Output option *--ambiguous*
590
591 * **Write all reads that could not be aligned to a file**
592
593 | Write all reads that could not be aligned to a file in the output directory. Written reads will appear as they did in the input, without any translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping) are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
594 |
595 | Output option *-un/--unmapped*
596
597 * **Offer all report files concatenated in one file**
598
599 | Prints out a Bismark mapping report
600
601 ]]>
602 </help>
603 <citations>
604 <citation type="doi">10.1093/bioinformatics/btr167</citation>
605 </citations>
606 </tool>