Mercurial > repos > jjohnson > rmats

comparison rmats.xml @ 1:74af9ab1a154 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 77429eedace24dcb2ebf8e209fce1515d2adb055-dirty"
author jjohnson
date Tue, 26 Jul 2022 16:21:33 +0000
parents ff15d6def09b
children
comparison
equal deleted inserted replaced
0:ff15d6def09b 1:74af9ab1a154
254 <output name="summary" file="novel/summary.txt" ftype="tabular"/> 254 <output name="summary" file="novel/summary.txt" ftype="tabular"/>
255 </test> 255 </test>
256 256
257 </tests> 257 </tests>
258 <help><![CDATA[ 258 <help><![CDATA[
259 ** rMATS ** 259 **rMATS**
260 260
261 RMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. 261 RMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
262 262
263
264 **INPUTS**
265
266 BAM files
267
268 Reads can be mapped independently of rMATS with any aligner and then the resulting BAM files can be used as input to rMATS. rMATS requires aligned reads to match --readLength unless --variable-read-length is given. rMATS also ignores alignments with soft or hard clipping unless --allow-clipping is given.
269
263 https://github.com/Xinglab/rmats-turbo#starting-with-bam-files 270 https://github.com/Xinglab/rmats-turbo#starting-with-bam-files
264 271
272
273 **OUTPUTS**
274
265 https://github.com/Xinglab/rmats-turbo#output 275 https://github.com/Xinglab/rmats-turbo#output
276
277 **Splicing Events**
278
279 .. image:: rmats_diagram.png
280 :height: 562
281 :width: 815
282
283
284 Each alternative splicing event type has a corresponding set of output files. In the filename templates below [AS_Event] is replaced by one of [SE (skipped exon), MXE (mutually exclusive exons), A3SS (alternative 3' splice site), A5SS (alternative 5' splice site), RI (retained intron)] for the event specific filename.
285
286
287 Output Files:
288 * summary.txt: Brief summary of all AS event types. Includes the total event counts and significant event counts. By default, events are counted as significant if FDR <= 0.05.
289 * [AS_Event].MATS.JC.txt: Final output including only reads that span junctions defined by rmats (Junction Counts)
290 * [AS_Event].MATS.JCEC.txt: Final output including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts)
291 * fromGTF.[AS_Event].txt: All identified alternative splicing (AS) events derived from GTF and RNA
292 * fromGTF.novelJunction.[AS_Event].txt: Alternative splicing (AS) events which were identified only after considering the RNA (as opposed to analyzing the GTF in isolation). This does not include events with an unannotated splice site.
293 * fromGTF.novelSpliceSite.[AS_Event].txt: This file contains only those events which include an unannotated splice site. Only relevant if --novelSS is enabled.
294 * JC.raw.input.[AS_Event].txt: Event counts including only reads that span junctions defined by rmats (Junction Counts)
295 * JCEC.raw.input.[AS_Event].txt: Event counts including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts)
296
297 Shared columns:
298 * ID: rMATS event id
299 * GeneID: Gene id
300 * geneSymbol: Gene name
301 * chr: Chromosome
302 * strand: Strand of the gene
303 * IJC_SAMPLE_1: Inclusion counts for sample 1. Replicates are comma separated
304 * SJC_SAMPLE_1: Skipping counts for sample 1. Replicates are comma separated
305 * IJC_SAMPLE_2: Inclusion counts for sample 2. Replicates are comma separated
306 * SJC_SAMPLE_2: Skipping counts for sample 2. Replicates are comma separated
307 * IncFormLen: Length of inclusion form, used for normalization
308 * SkipFormLen: Length of skipping form, used for normalization
309 * PValue: Significance of splicing difference between the two sample groups. (Only available if the statistical model is on)
310 * FDR: False Discovery Rate calculated from p-value. (Only available if statistical model is on)
311 * IncLevel1: Inclusion level for sample 1. Replicates are comma separated. Calculated from normalized counts
312 * IncLevel2: Inclusion level for sample 2. Replicates are comma separated. Calculated from normalized counts
313 * IncLevelDifference: average(IncLevel1) - average(IncLevel2)
314 Event specific columns (event coordinates):
315 * SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
316 + The inclusion form includes the target exon (exonStart_0base, exonEnd)
317 * MXE: 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd upstreamES upstreamEE downstreamES downstreamEE
318 + If the strand is + then the inclusion form includes the 1st exon (1stExonStart_0base, 1stExonEnd) and skips the 2nd exon
319 + If the strand is - then the inclusion form includes the 2nd exon (2ndExonStart_0base, 2ndExonEnd) and skips the 1st exon
320 * A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
321 + The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
322 * RI: riExonStart_0base riExonEnd upstreamES upstreamEE downstreamES downstreamEE
323 + The inclusion form includes (retains) the intron (upstreamEE, downstreamES)
266 324
267 ]]></help> 325 ]]></help>
268 <expand macro="citations" /> 326 <expand macro="citations" />
269 </tool> 327 </tool>