Entering edit mode
6.6 years ago
qudrat
▴
100
Is it necessary to filter mitochondrial reads from BAM file before I proceed to Cufflinks? If I filter the mitochondrial reads, the BAM file size get reduced and it takes less time to complete Cufflinks. Would it affect the final results?
It really depends on the aim of your experiment, are you interested in looking at the mitochondrial gene expressions?
My aim is to find novel transcripts from chromosomal genes
If you just want novel transcripts, then it should not make any difference including chrM.