running multiple RSeQC jobs
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4.6 years ago
Apoorva ▴ 330

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 • 2.0k views
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Check GNU parallel, see the posts here, here and here

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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.

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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?