running multiple RSeQC jobs
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
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Check GNU parallel, see the posts here, here and here
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.
But the
tin.pyis quite slow in computingTINas 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 myBAMfile into smaller BAM files based on chromosomes and then performtin.pyqc?