FAIRE for non-standard cultivar, mapping to reference, MAPQ
I have FAIRE-seq data from two cultivars: reference B73 and less known S68.
I assumed I can align reads from both cultivars to B73 reference sequence, which is standard.
bbmap with default settings.
I've seen, that MAPQ>10 read filtering is frequently applied.
The problem is, that (I think) too low percentage of reads pass this filter. It is ca. 50-60% for B73, which I assume should be mapped very well, and ca. 40-48% for S68.
I have folowing questions:
- What settings, for example for
bwa memare good for alignment of chromatin-level data from non-standard cultivar to reference genome?
- What MAPQ threshold should I apply?
- I haven't filtered
fastqfiles for base qualities (looks good in
fastqcafter adapter removal). Should I do this filtering?
Here are MAPQ plots from
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