I am trying to plot coverage for CDS region using deeptools.
from the manual there is a flag --region
, but it either takes a chromosome or region of chromosome
–region chr10 or –region chr10:456700:891000
Is there is a way to pass bed file to it like in –blackListFileName, -bl
flag?
or I need to use something like:
samtools view -hL cds.bed alignment.bam > alignment_in_cds.sam
and then use plotCoverage normally?
I think this should be another question, but I would like it to be consistent with the post.
Is there a way to increase the scale of the "fraction of bases sampled" axis? in the example from documentation I could figure out that 5% of sample was covered 0 time; but what if there is more! can I control the scale to see it?
Not currently, it's just whatever matplotlib chooses, but you can save the values (
--outRawCounts
) and then do the plotting however you'd like in R.