running multiple RSeQC jobs

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7.4 years ago

AB ▴ 360

Hi all,

I want to check the integrity of my RNA-Seq samples. I usually use tin.py in the RSeQC package for this purpose. But its very slow. Is there an alternate tool or software I can use ? Or is there a parameter I can add to run it for multiple bam files simultaneously ?

Thanks

RNA-Seq RSeQC tin.py • 3.2k views

ADD COMMENT • link updated 7.3 years ago by Biostar 20 • written 7.4 years ago by AB ▴ 360

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Check GNU parallel, see the posts here, here and here

ADD REPLY • link 7.4 years ago by h.mon 35k

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Is RSeQC running slowly because it is spending its time reading files or analyzing them? GNU Parallel won't get around I/O-bound work.

ADD REPLY • link 7.3 years ago by Alex Reynolds 36k

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But the tin.py is quite slow in computing TIN as it processes transcripts sequentially. I have a large BAM file of ~35 GB. It took 18 hours to process that. Is there a way to speed it up using multithreading or multiprocessing? Should I split up my BAM file into smaller BAM files based on chromosomes and then perform tin.py qc?

ADD REPLY • link 4.2 years ago by Abhishek Shakya • 0

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