Cufflinks with large BAM file

Question

[qudrat]

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?

[Renesh]

Cufflinks should not hang with 10GB bam file. What computer are you using?

[qudrat]

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

[Kevin Blighe]

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