Question: Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
0
gravatar for thecuriousbiologist
7.2 years ago by
United States
thecuriousbiologist480 wrote:

Hi,

I wish to plot per chromosome coverage from a BAM file obtained from aligning exome sequencing data.

Are there any good R packages/any other non-R packages that can quickly get me such plots ?

I was planning to use samtools to generate pileup files and then go on from there, however that would take a long time.

Any suggestions would be much appreciated.

Thank you.

chromosome coverage plot • 7.1k views
ADD COMMENTlink modified 7.1 years ago • written 7.2 years ago by thecuriousbiologist480
3
gravatar for William
7.2 years ago by
William4.6k
Europe
William4.6k wrote:

Qualimap is a very good and easy to use quality assurance tool for use on BAM files. It gives you a lot of statistics and plots, including coverage on all the chromosomes, in numbers and in plots.

http://qualimap.bioinfo.cipf.es/

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by William4.6k

Thanks. Yes, I did finally move on to Qualimap. I ran it on some small datasets and the reports look good. !

ADD REPLYlink written 7.2 years ago by thecuriousbiologist480
1
gravatar for thecuriousbiologist
7.1 years ago by
United States
thecuriousbiologist480 wrote:

When Qualimap reports the per chromosome mean coverage, does it normalize by the size of the chromosome ? I have certain chromosomes where I always get a low coverage as compared to others ?

ADD COMMENTlink written 7.1 years ago by thecuriousbiologist480
1

It is the mapped bases divided by the length of the chromosome ( the previous 2 columns). Maybe it is a more difficult chromosome to sequence / map.

http://qualimap.bioinfo.cipf.es/doc_html/analysis.html#bam-qc

ADD REPLYlink written 7.1 years ago by William4.6k

Please note that if an annotation is provided, since version 0.7 the coverage will be normalized by the length of all the regions in the corresponding chromosome. Please see this thread for more information: https://groups.google.com/d/msg/qualimap/AO_6111Gg1E/-oey1kAs6GcJ

ADD REPLYlink written 7.1 years ago by Fennan30
0
gravatar for Gabriel R.
7.2 years ago by
Gabriel R.2.7k
Danmarks Tekniske Universitet
Gabriel R.2.7k wrote:

You can just put the depth column from mpileup into a text file and use the density() function in R to plot it. If you have to do it over and over again, write yourself a little perl script.

ADD COMMENTlink written 7.2 years ago by Gabriel R.2.7k
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