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Cufflinks Crashes Because Of Mitochondrial Rna Abundance

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.

cufflinks rna
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updated by sunil.mangalam • sunil.mangalam • written by M K M K

2 answers

remove your reads mapped to chrM using

 samtools view -b -o nochrm.bam  -L everything_but_chrM.bed your.bam
• 34 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by M K M K

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?

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written by sunil.mangalam • sunil.mangalam

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