Entering edit mode
7.2 years ago
rishi
▴
10
Hi. Newbie here.
I ran a bowtie2 alignment in default, very sensitive, and changed -DLRN (-D 20 -R 2 -N 0 -L 32 -i S,1,0.35) parameters. After running qualimap bamqc I'm getting same coverage across reference for all my bowtie2 runs, with similar low coverage areas (going down from 40 to 5) in all of them. The alignment is done on Mtb genome. It seems the alignment is getting GC biased. How do I make my alignment better? https://postimg.org/image/vj54tdmt9/ https://postimg.org/image/d3wqnxyod/
What makes you think the alignment is biased? It's rather more likely that it's the sequencing itself. Anyway, what is your end goal of eliminating the GC bias?
I am getting some regions with very low alignment/coverage, as evident in the images. What can I do about it?
Probably nothing. That's very normal. Sequencing itself, as said by Devon Ryan, is biased against GC-rich sequences.
How do I set a filter so that bowtie2 neglects multiple alignment and reports only one map for each seed, i.e. the one with the best alignment score?
That's the default.