Yes, always map on full genome, then filter.
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Carlo Yague
Is it better to remove MT reads by removing the MT Chromosome from your fasta or removing aligned MT reads post alignment?
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!
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Vivek
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datascientist28
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datascientist28
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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.
Yeah that's what I was thinking but just wanted to check thanks. Thank you!
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