Hello,
While using the Tophat --> htseq-count --> DESeq pipeline, I'm finding that htseq-count slams my machine (8 GB RAM). I'm guessing that since it is using all memory, and even most swap memory, that perhaps I could improve the performance by breaking down the task somehow. I'm using version 0.5.3p3 with these options:
htseq-count -m intersection-nonempty -s no -t CDS -i gene_id -o htseq_{$fprefix}.sam sorted_{$fprefix}.sam hg19_EnsGene.gff
Would it help if I separated the input files by chromosome ?
Thanks,
Danielle
While using the Tophat --> htseq-count --> DESeq pipeline, I'm finding that htseq-count slams my machine (8 GB RAM). I'm guessing that since it is using all memory, and even most swap memory, that perhaps I could improve the performance by breaking down the task somehow. I'm using version 0.5.3p3 with these options:
htseq-count -m intersection-nonempty -s no -t CDS -i gene_id -o htseq_{$fprefix}.sam sorted_{$fprefix}.sam hg19_EnsGene.gff
Would it help if I separated the input files by chromosome ?
Thanks,
Danielle
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