Covarage X not per base coverage. As a whole
1
0
Entering edit mode
5 weeks ago
Edmond • 0

Hello,

Before anyone marks this post as "duplicated" from this post.

This post and plotCoverage from deeptools, gives us the mean coverage ( or coverage) per base. Thus, if I want a coverage, like 100X, which is typically for WES, ( I am trying to replicate results that effectively give 100X) from a quality- filter with removed duplicates.

Also, I have tried to cover the exon regions from the primary assembly, however, these results give me ~ 17 Coverage.

How can I convert whis per base mean coverage, to give me 100X more or less ?

Furthermore, plotCoverage, plots a log-like distribution, however, the results I want to obtain follows a normal distribution, with a mean of 100X

It has to be mentioned that this plot is in percetange region.

enter image description here

bedtools plotCoverage samtools • 211 views
ADD COMMENT
0
Entering edit mode
5 weeks ago
samtools depth -b capture.bed -a in.bam | awk '{N+=int($3);} END {print N/NR;} '
ADD COMMENT
0
Entering edit mode

This answer it does not help. It is the same as the link I provided. The only thing It approaches to my answer is with bedtools:

bedtools coverage -hist -b 152611.qual.rmdup.bam -a exones.sort.bed -g hg19.genome -sorted -header >hist.txt

Similar as in here But in the link, they put the options -b as the captured.bed i.e the region of interest. However, on mu line, is the other way around, Furthemore, do you know why do they compute 1-cumsum ?

ADD REPLY

Login before adding your answer.

Traffic: 2471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6