Entering edit mode
6.6 years ago
qudrat
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100
I have a TopHat large BAM file of 10GB and when I do Cufflinks with this 10GB file it takes too much time and eventually it hangs. Is it possible to split this file chromosome-wise and with smaller BAM file Cufflinks is done?
Cufflinks should not hang with 10GB bam file. What computer are you using?
Its a ubuntu 16.10 with 16GB RAM. But not all 10GB bam file hangs. I think there is some problem in BAM file that is why i wanted to split
I think that it's okay to split the BAM file by chromosome and to then analyse them independently in Cufflinks. Take a look here: How To Split A Bam File By Chromosome