Cufflinks Crashes Because Of Mitochondrial Rna Abundance

Question

[M K]

Hi All,

When I tried to run Cufflinks it was crashed, and I found that because of Mitochondrial RNA abundance that mapped to human genome. Dose any one have any idea about removing Mitochondrial RNA from the the accepted.hit.bam file to use it with Cufflinks.

Answer 1

[Pierre Lindenbaum]

remove your reads mapped to chrM using

 samtools view -b -o nochrm.bam  -L everything_but_chrM.bed your.bam

[M K]

Hi Pierre, Thanks for your help. Is -L everything_but_chrM.bed your.bam the input file (= accepted.hits.bam).

Answer 2

[sunil.mangalam]

Hi,

We recently had a similar experience with cufflinks running out of memory and crashing. Our library also has mitochondrial RNA reads. Can you please share what error you had?