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comparison bismark_mapping/bismark_bowtie2_wrapper.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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6:0f8646f22b8d 7:fcadce4d9a06
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.16.3">
2
3 <description>Bisulfite reads mapper</description>
4 <!--<version_command>bismark version</version_command>-->
5 <requirements>
6 <requirement type="package" version="0.1.19">samtools</requirement>
7 <requirement type="package" version="2.1.0">bowtie2</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <regex match="Error:" />
13 <regex match="Exception:" />
14 </stdio>
15 <command interpreter="python">
16 <![CDATA[
17 bismark_wrapper.py
18
19 ## Change this to accommodate the number of threads you have available.
20 --num-threads "\${GALAXY_SLOTS:-24}"
21
22 ##--bismark_path \$SCRIPT_PATH
23 --bismark_path "$__tool_directory__"
24
25 --bowtie2
26
27 ##
28 ## Bismark Genome Preparation, if desired.
29 ##
30
31 ## Handle reference file.
32 #if $refGenomeSource.genomeSource == "built_in_fasta":
33 --own-file="${refGenomeSource.built_in_fasta.fields.path}"
34 #else if $refGenomeSource.genomeSource == "own_fasta":
35 --own-file="$refGenomeSource['own_fasta']"
36 #else:
37 --indexes-path "${refGenomeSource.built_in_indexes.fields.path}"
38 #end if
39
40 ##
41 ## Input parameters
42 ##
43
44 #if $singlePaired.sPaired == "single":
45 --single-paired $singlePaired.input_singles
46
47 #if $singlePaired.input_singles.ext == "fastqillumina":
48 --phred64-quals
49 --fastq
50 #elif $singlePaired.input_singles.ext == "fastqsanger":
51 --fastq
52 #elif $singlePaired.input_singles.ext == "fasta":
53 --fasta
54 #end if
55 #else:
56 --mate-paired
57 #set $mate1 = list()
58 #set $mate2 = list()
59 #for $mate_pair in $singlePaired.mate_list
60 $mate1.append( str($mate_pair.input_mate1) )
61 $mate2.append( str($mate_pair.input_mate2) )
62 #end for
63
64 --mate1 #echo ','.join($mate1)
65 --mate2 #echo ','.join($mate2)
66
67 #for $mate_pair in $singlePaired.mate_list:
68 #if $mate_pair.input_mate1.ext == "fastqillumina":
69 --phred64-quals
70 --fastq
71 #elif $mate_pair.input_mate1.ext == "fastqsanger":
72 --fastq
73 #elif $mate_pair.input_mate1.ext == "fasta":
74 --fasta
75 #end if
76 #break
77 #end for
78
79 -I $singlePaired.minInsert
80 -X $singlePaired.maxInsert
81 #end if
82
83 #if $sort_bam:
84 --sort-bam
85 #end if
86
87 ## for now hardcode the value for the required memory per thread in --best mode
88 --chunkmbs 512
89
90
91 #if $params.settingsType == "custom":
92
93 ## default 20
94 --seed-len $params.seed_len
95 ## default 0
96 --seed-mismatches $params.seed_mismatches
97 ## default 15
98 --seed-extention-attempts $params.seed_extention_attempts
99 ## default 2
100 --max-reseed $params.max_reseed
101
102 ## default 70
103 ##--maqerr $params.maqerr
104
105 ## default unlimited
106 #if $params.qupto != 0:
107 --qupto $params.qupto
108 #end if
109 #if $params.skip_reads != 0:
110 --skip-reads $params.skip_reads
111 #end if
112
113 ## if set, disable the original behaviour
114 $params.no_mixed
115 ## if set, disable the original behaviour
116 $params.no_discordant
117
118 #if $params.bismark_stdout:
119 --stdout "$output_stdout"
120 #end if
121
122 #if $params.isReportOutput:
123 --output-report-file "$report_file"
124 #end if
125
126 #else:
127 --output-report-file "$report_file"
128 #end if
129
130 ##
131 ## Output parameters.
132 ##
133 --output $output
134 ##$suppress_header
135
136 #if str( $singlePaired.sPaired ) == "single"
137 #if $output_unmapped_reads_l
138 --output-unmapped-reads "$output_unmapped_reads_l"
139 #end if
140 #if $output_suppressed_reads_l
141 --output-suppressed-reads "$output_suppressed_reads_l"
142 #end if
143 #else
144 #if $output_unmapped_reads_l and $output_unmapped_reads_r
145 --output-unmapped-reads-l "$output_unmapped_reads_l"
146 --output-unmapped-reads-r "$output_unmapped_reads_r"
147 #end if
148 #if $output_suppressed_reads_l and $output_suppressed_reads_l
149 --output-suppressed-reads-l "$output_suppressed_reads_l"
150 --output-suppressed-reads-r "$output_suppressed_reads_r"
151 #end if
152 #end if
153
154 ]]>
155 </command>
156 <inputs>
157 <conditional name="refGenomeSource">
158 <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">
159 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
160 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
161 <option value="own_fasta">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
162 </param>
163 <when value="built_in_indexes">
164 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)" help="If your genome of interest is not listed, contact your Galaxy admin">
165 <options from_data_table="bismark_indexes">
166 <filter type="sort_by" column="name"/>
167 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
168 </options>
169 </param>
170 </when>
171 <when value="built_in_fasta">
172 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
173 <options from_data_table="all_fasta">
174 <filter type="sort_by" column="name"/>
175 <validator type="no_options" message="No genomes in fasta are available for the selected input dataset"/>
176 </options>
177 </param>
178 </when>
179 <when value="own_fasta">
180 <param name="own_fasta" type="data" format="fasta" label="Select the reference genome"/>
181 </when>
182 </conditional>
183
184 <!-- Input Parameters -->
185 <conditional name="singlePaired">
186 <param name="sPaired" type="select" label="Is this library mate-paired?">
187 <option value="single">Single-end</option>
188 <option value="paired">Paired-end</option>
189 </param>
190 <when value="single">
191 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
192 </when>
193 <when value="paired">
194 <repeat name="mate_list" title="Paired End Pairs" min="1">
195 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
196 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
197 </repeat>
198 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
199 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
200 </when>
201 </conditional>
202
203 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" 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" help="You can use the default settings or set custom values for any of Bismark's parameters.">
207 <option value="default">Use Defaults</option>
208 <option value="custom">Full parameter list</option>
209 </param>
210 <!--<when value="default" />-->
211 <!-- Full/advanced params. -->
212 <when value="custom">
213 <!-- -N -->
214 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
215 <!-- -L -->
216 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
217 <!--
218 <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'." />
219 -->
220 <!-- -D -->
221 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
222 <!-- -R -->
223 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
224
225 <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'." />
226 <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" />
227
228 <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 (only for paired-end reads)" help="" />
229 <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 (only for paired-end reads" help="" />
230
231 <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." />
232 <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" />
233 <!-- output Options -->
234 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
235 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Offer all report files concatenated in one file (Mapping Report)" />
236
237 <!--end output options -->
238 </when> <!-- full -->
239 </conditional> <!-- params -->
240 <!--
241 <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." />
242 -->
243 </inputs>
244
245
246 <outputs>
247 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
248 <filter>
249 ((
250 params['settingsType'] == "default" or
251 ( params['settingsType'] == "custom" and
252 params['isReportOutput'] is True )
253 ))
254 </filter>
255 </data>
256 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
257 <filter>
258 ((
259 params['settingsType'] == "custom" and
260 params['bismark_stdout'] is True
261 ))
262 </filter>
263 </data>
264
265 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
266 <actions>
267 <conditional name="refGenomeSource.genomeSource">
268 <when value="built_in_indexes">
269 <action type="metadata" name="dbkey">
270 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
271 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
272 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
273 </option>
274 </action>
275 </when>
276 <when value="generate_indexes">
277 <action type="metadata" name="dbkey">
278 <option type="from_data_table" name="all_fasta" column="1" offset="0">
279 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
280 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
281 </option>
282 </action>
283 </when>
284 </conditional>
285 </actions>
286 </data>
287
288 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
289 <filter>
290 ((
291 params['settingsType'] == "custom" and
292 params['suppressed_read_file'] is True
293 ))
294 </filter>
295 <actions>
296 <conditional name="singlePaired.sPaired">
297 <when value="single">
298 <action type="format">
299 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
300 </action>
301 </when>
302 </conditional>
303 </actions>
304 </data>
305
306 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
307 <filter>
308 ((
309 singlePaired['sPaired'] == "paired" and
310 params['settingsType'] == "custom" and
311 params['suppressed_read_file'] is True
312 ))
313 </filter>
314 <actions>
315 <conditional name="singlePaired.sPaired">
316 <when value="single">
317 <action type="format">
318 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
319 </action>
320 </when>
321 <when value="paired">
322 <!--action type="format">
323 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
324 </action-->
325 </when>
326 </conditional>
327 </actions>
328 </data>
329
330 <!-- Outout unmapped reads -->
331 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
332 <filter>
333 ((
334 params['settingsType'] == "custom" and
335 params['unmapped_read_file'] is True
336 ))
337 </filter>
338 <actions>
339 <conditional name="singlePaired.sPaired">
340 <when value="single">
341 <action type="format">
342 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
343 </action>
344 </when>
345 <when value="paired">
346 <!--action type="format">
347 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
348 </action-->
349 </when>
350 </conditional>
351 </actions>
352 </data>
353
354 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
355 <filter>
356 ((
357 singlePaired['sPaired'] == "paired" and
358 params['settingsType'] == "custom" and
359 params['unmapped_read_file'] is True
360 ))
361 </filter>
362 <actions>
363 <conditional name="singlePaired.sPaired">
364 <when value="single">
365 <action type="format">
366 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
367 </action>
368 </when>
369 <when value="paired">
370 <!--action type="format">
371 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
372 </action-->
373 </when>
374 </conditional>
375 </actions>
376 </data>
377 </outputs>
378
379 <tests>
380 </tests>
381
382 <help>
383 <![CDATA[
384
385 **What it does**
386
387 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome.
388 | 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).
389 | 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).
390 | 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.
391 |
392 | 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.
393 |
394 | 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.
395
396 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
397
398 ----
399
400 **Know what you are doing**
401
402 .. class:: warningmark
403
404 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco.
405 | In other words = running this tool with default parameters will probably not give you meaningful results.
406 | A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
407 |
408
409 .. class:: warningmark
410
411 | 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.
412
413 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
414
415 ----
416
417 **Input formats**
418
419 | 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.
420
421 ----
422
423 **A Note on Built-in Reference Genomes**
424
425 | 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.
426 | 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.
427 | 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.
428
429 ----
430
431 **Outputs**
432
433 * The final output of Bismark is in SAM format by default, and has the following columns::
434
435 Column Description
436 -------- --------------------------------------------------------
437 1 QNAME seq-ID
438 2 FLAG this flag tries to take the strand a bisulfite read
439 originated from into account
440 (this is different from ordinary DNA alignment flags!)
441 3 RNAME chromosome
442 4 POS start position
443 5 MAPQ always 255
444 6 CIGAR extended CIGAR string
445 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
446 8 MPOS 1-based Mate POSition
447 9 ISIZE Inferred insert SIZE
448 10 SEQ query SEQuence on the same strand as the reference
449 11 QUAL Phred33 scale
450 12 NM-tag edit distance to the reference)
451 13 XX-tag base-by-base mismatches to the reference.
452 This does not include indels.
453 14 XM-tag methylation call string
454 15 XR-tag read conversion state for the alignment
455 16 XG-tag genome conversion state for the alignment
456
457
458 | Each read of paired-end alignments is written out in a separate line in the above format.
459 |
460
461 * It looks like this (scroll sideways to see the entire example)::
462
463 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
464 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
465 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
466
467 ----
468
469 **Note on Bismark settings**
470
471 | 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.
472
473 ----
474
475 **Bismark settings**
476
477 * **If Paired-End Reads**
478
479 * **Minimum insert size for valid paired-end alignments**
480
481 | 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.
482 |
483 | Alignment option *-I/--minins <INT>*
484
485
486 * **Maximum insert size for valid paired-end alignments**
487
488 | 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.
489 |
490 | Alignment option *-X/--maxins <INT>*
491
492
493 * **Number of mismatches to be allowed in a seed alignment during multiseed alignment**
494
495 | 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).
496 |
497 | Bowtie 2 Specific option *-N <INT>*
498
499 * **Length of the seed substrings to align during multiseed alignment**
500
501 | 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).
502 |
503 | Bowtie 2 Specific option *-L <INT>*
504
505
506 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on**
507
508 | 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.
509 |
510 | Bowtie 2 Effort option *-D <INT>*
511
512 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
513
514 | <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.
515 |
516 | Bowtie 2 Effort option *-R <INT>*
517
518 * **Only aligns the first N reads or read pairs from the input**
519
520 | Only aligns the first <int> reads or read pairs from the input. Default: no limit.
521 |
522 | Input option *-u/--upto <INT>*
523
524 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
525
526 | Input option *-s/--skip*
527
528 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
529
530 | 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.
531 |
532 | Bowtie 2 Paired-End option *--no-discordant*
533
534 * **Disable Bowtie 2's behaviour to try to find alignments for the individual mates**
535
536 | 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.
537 |
538 | Bowtie 2 Paired-End option *--no-mixed*
539
540 * **Write ambiguous reads to an extra output file**
541
542 | 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.
543 |
544 | Output option *--ambiguous*
545
546 * **Write all reads that could not be aligned to a file**
547
548 | 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.
549 |
550 | Output option *-un/--unmapped*
551
552 * **Offer all report files concatenated in one file**
553
554 | Prints out a Bismark mapping report
555
556 ]]>
557 </help>
558 <citations>
559 <citation type="doi">10.1093/bioinformatics/btr167</citation>
560 </citations>
561 </tool>