I am running Cuffdiff on our server, as follows:
./cuffdiff -o diff_out -b Bowtie2Index/genome.fa -p 8 --library-type fr-firststrand -L control,LS -u genes.gtf \ ./result/CTR/accepted_hits.bam ./result/LS/accepted_hits.bam
where the two BAM files are the outputs from two Tophat2 runs on hg19 (using GENCODE annotation) with paired-end reads.
In “Calculating preliminary abundance estimates”, Cuffdiff processed 34053 loci.
At the step “Testing for differential expression and regulation in locus”, Cuffdiff became extremely slow: after 24 hours, it just progressed from:
Processing Locus chr1:33772366-33896653 [ ] 1%
Processing Locus chr1:108614103-108617141 [* ] 4%
Is this normal?
Is there a way to speed up this process?
I’d greatly appreciate any ideas and suggestions.
Thank you very much!