Running cufflinks per chromosome

Question

[vrehaman]

Dear Team,

I have gone through some biostar posts related to cufflinks and suggesting not to run cufflinks per chromosome basis. I have used multithreading option too. But still it is very time consuming.

Is there any way to speedup the quantification and differential expression using cufflinks and cuffdiff.

Please let me know your suggestions.

Thanks & Regards Fazulur Rehaman

Answer 1

[Arup Ghosh]

If you are only looking into differentially expressed genes I will suggest you use FeatureCounts to get raw read counts and go fro analysis using DESeq2 or edgeR. The process will much faster than cufflinks+cuffdiff combo. Also, you cant use Stringtie and Ballgown for differential expression analysis.

[vrehaman]

Thanks a lot Arup. I will try that.

Thanks & Regards Fazulur Rehaman