Hi all,
I'm running cufflinks with the mask option:
but I still end up with, for instance, relatively high (and variable) FPKMs in mitochondrial genes, which should be filtered out from the reads.
I did find an old, essentially un-answered post on this forum mentioning a similar issue; anyone have any other deep insight?
I'm running cufflinks with the mask option:
Code:
cufflinks --num-threads 50 --output-dir analysis-multi/CaS3A -u -M Reference/AAA/suspect.gtf --frag-bias-correct Reference/AAA/mel_only.fa -G Reference/AAA/mel_only.gtf analysis-multi/CaS3A/assigned_dmel_rescued.bam
Code:
$ grep mt:tRNA:K mel_only.gtf dmel_dmel_mitochondrion_genome FlyBase exon 3768 3838 . + . transcript_id "FBtr0100864"; gene_id "FBgn0013697"; gene_name "mt:tRNA:K"; $ grep mt:tRNA:K suspect.gtf dmel_dmel_mitochondrion_genome FlyBase exon 3768 3838 . + . transcript_id "FBtr0100864"; gene_id "FBgn0013697"; gene_name "mt:tRNA:K";
Comment