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rMATS 4.x.x paired analysis #14551

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mhebrard opened this issue Apr 22, 2019 · 1 comment

mhebrard commented

As discussed with @dpryan79 on gitter,
rMATS v4 do not integrate paired analysis anymore.
from google groups :

The paired sample analysis has not yet been implemented in 4.0.1. You can generate the counts using 4.0.1 then use the paired analysis code either in 3.2.5 or in https://github.com/Xinglab/rMATS-STAT.

could we integrate the .py scripts ? particularly

rMATS_paired.py
FDR.py

then:

from the raw inputs files we can add the Pvalue

python rMATS_paired.py JC.raw.input.SE.txt out/ 1 0.1

from the file with Pvalue we can add the FDR

python FDR.py out/rMATS_Result_P.txt /out/rMATS_Result_F.txt

from the file with FDR we need to merge the event location and calculate the Inclusion levels

The text was updated successfully, but these errors were encountered:

Contributor

tseemann commented

rmats 4.0.2 is now in conda.
does this resolve the problem @mhebrard ?
if so , can you please close this issue?
thank you.

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