This is a test version of Biostars. For the public version, visit https://www.biostars.org.
pileup consolidation tool

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
• 1,267 views • link
written by noodle noodle

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

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Detection of RNA modifications.

• 0 views • link
written by noodle noodle

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?

• 0 views • link
written by noodle noodle

0 answers

No answers yet.

Log in to answer this question.

More posts like this