What/where is *.MATS.ReadsOnTargetAndJunctionCounts.txt?

[Neil Kuehnle]

I was looking at testing out rMAPs to do some exploratory motif analysis and it mentions wanting files like SE.MATS.ReadsOnTargetAndJunctionCounts.txt.

My output w/ rMats Turbo 4.1.1 doesn't include these files. Is this an older name? Looking over the documentation it seems like the the *.MATS.JC.txt or *.MATS.JCEC.txt would have the correct info? Is this purely a legacy naming thing or are the structure of these output files different?

[kutsc...@gmail.com]

The rMAPS quick run guide (http://rmaps.cecsresearch.org/Help/QuickRun/) has example data to download which includes the files CLIPMap.test.rMATS.txt and motifMap.testEvents.rMATS.txt. Those files have the same format as the output file SE.MATS.JC.txt from rMATS v4.1.1. Based on that, it seems that rMAPS is compatible with the v4.1.1 output

Looking at the documentation for older rMATS versions it does seem that the names of the output files were changed but based on the descriptions the format stayed the same:
rMATS 3.2.5 documentation uses AS_Event.MATS.JunctionCountOnly.txt and AS_Event.MATS.ReadsOnTargetAndJunctionCounts.txt: http://rnaseq-mats.sourceforge.net/rmats3.2.5/user_guide.htm#output

rMATS 4.0.1 documentation uses AS_Event.MATS.JC.txt and AS_Event.MATS.JCEC.txt: http://rnaseq-mats.sourceforge.net/rmats4.0.1/user_guide.htm#output

Eric