pileup consolidation tool
0
0
Entering edit mode
5 weeks ago
joe ▴ 380

Hello Biostars,

I'm looking for a pileup tool that will consolidate output to a table that is strand sensitive, separates +/-, includes indels as well count of starts and stops. I'm familiar with many tools, but it seems like none of them are able to capture everything listed. JACUSA2 is the closest I've found but this doesn't have al the features. I've included an example header below for what I'm after. Thanks!

chr loc ref strand  A   T   C   G   a   t   c   g   Insertion   Deletion    Stops   Starts
1   888659  T   +   0   9   0   2   0   0   0   0   2:AG|1:AGAG 1:ATT   3   2

RNAseq pileup jacusa samtools • 253 views
0
Entering edit mode

what is the scientific question you're trying to answer ?

0
Entering edit mode

Detection of RNA modifications.

0
Entering edit mode

I tried to use Rsamtools::pileup() but haven't been able to come up with the right parameters to pass in PileupParam ...maybe somewhere here knows better?