Question: Calculating coverage for WGS, WES and RNASeq
0
gravatar for hihi.joshi
6 days ago by
hihi.joshi0
Australia
hihi.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 • 196 views
ADD COMMENTlink modified 6 days ago by Philipp Bayer4.6k • written 6 days ago by hihi.joshi0
0
gravatar for finswimmer
6 days ago by
finswimmer410
Germany
finswimmer410 wrote:

Hello,

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

fin swimmer

ADD COMMENTlink written 6 days ago by finswimmer410
0
gravatar for trausch
6 days ago by
trausch730
Germany
trausch730 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 6 days ago by trausch730
0
gravatar for Philipp Bayer
6 days ago by
Philipp Bayer4.6k
Australia/Perth/UWA
Philipp Bayer4.6k 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 6 days ago by Philipp Bayer4.6k
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