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8 years ago I’ve created an initial pipeline that follows Anshul Kundaje’s method. The
goal was to automate as much as possible and make it easy to use.
it’s currently available for testing on hpcc at:
/home/uec-00/ramjan/devel/encodePipeline/wrap_encode_pipeline.pl
all you supply are the initial bams, for example:
wrap_encode_pipeline.pl -control control.bam -treated sample1.bam -treated
sample2.bam
you can supply as many “-control” or “-treated” as needed (i.e. 1 or
more)
My tool will handle:
tagAlign conversion
pooling of replicates
creation of pseudoreplicates both with and without pooling (through random
splitting)
SPP peak calling on all the above combinations (i.e. pooled, replicates,
pseudoreps, pooled pseudoreps)
IDR analysis on all relevant combinations (i.e. pooled, replicates,
pseudoreps, pooled pseudoreps)
The most intense step is SPP peak calling, so it’s been multithreaded to run
as parallel as possible.
The resulting data and reports are clearly organized. You can see the order of
operations, as well as the dependencies and outputs for each step.
let me know of any issues, if all goes well, we will make it available to all
users.
-zackOriginal comment by zack...@gmail.com on 12 May 2014 at 10:29
- Changed state: Testing
Original issue reported on code.google.com by
zack...@gmail.comon 13 Mar 2014 at 12:27