Is it better to remove MT reads by removing the MT Chromosome from your fasta or removing aligned MT reads post alignment?

Question

[datascientist28]

Doing an ATAC project, is it bad practice to remove MT reads by removing the MT Chromosome from your fasta (and subsequent index) or removing aligned MT reads post alignment? and Why?

Thanks!

Answer 1

[Vivek]

My intuition would be that removing the chromosome from the BAM file post-alignment is probably the better choice, otherwise the reads that would find better alignment to the MT chromosome would end up aligning to their second best region in the fasta to increase the possibility of mis-mapped reads and subsequently give you false positive variants.

[Carlo Yague]

Yes, always map on full genome, then filter.

[datascientist28]

Yeah that's what I was thinking but just wanted to check thanks. Thank you!

[ATpoint]

I would also say that aligning to the full genome is better for the reasons mentioned above. Additionally, if you remove chrM you cannot distinguish if the unmapped reads are chrM or any other source of contamination, so better keep it and remove from the bam.