Question: Calculating coverage for WGS, WES and RNASeq
0
gravatar for Joshi
9 months ago by
Joshi0
Australia
Joshi0 wrote:

Hi,

I need some advise on calculating coverage

Basically for a set of BAM files, WGS, WES and RNA-Seq - I am interested in calculating and representing coverage - to show the contrast between these differing sequencing techniques (and limited to that ... not comparison). The coverage needs to be calculated at gene/exon level.

I am comfortable enough with determining the region of interest and extracting those regions from NCBI's Refseq.

However, I would appreciate some guidance around various coverage metrics for WGS, WES and RNA-Seq and what characteristics and limitations they have.

Needless to say, I am willing to do the background reading - but some guidance in this matter will help me understand the landscape.

Thanks, Himanshu

rna-seq wes coverage sequence wgs • 780 views
ADD COMMENTlink modified 9 months ago by Philipp Bayer5.5k • written 9 months ago by Joshi0
0
gravatar for finswimmer
9 months ago by
finswimmer2.9k
Germany
finswimmer2.9k wrote:

Hello,

my favorite is picard HSMetrics. There is also a detailed description of the metrics.

fin swimmer

ADD COMMENTlink written 9 months ago by finswimmer2.9k
0
gravatar for trausch
9 months ago by
trausch1.0k
Germany
trausch1.0k wrote:

You can try alfred (disclaimer: our own tool). Example plots are here: WGS and WES. It also supports feature counting for RNA-Seq.

ADD COMMENTlink written 9 months ago by trausch1.0k
0
gravatar for Philipp Bayer
9 months ago by
Philipp Bayer5.5k
Australia/Perth/UWA
Philipp Bayer5.5k wrote:

There's also mosdepth

The manual shows different options for exome/WGS etc. input, you can use a bed file of regions of interest to see only those. Preprint from 6 days ago: http://www.biorxiv.org/content/early/2017/09/07/185843

ADD COMMENTlink written 9 months ago by Philipp Bayer5.5k
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