Question: Ngsrich Output Explanation
0
gravatar for mark.dunning
6.4 years ago by
mark.dunning200
The University of Sheffield
mark.dunning200 wrote:

I am trying to use the NGSrich tool to compute and visualise enrichment of target regions in an exome-sequencing experiment.

http://sourceforge.net/projects/ngsrich/

The tool seems to produce some useful output to hand to my collaborators, but I am not clear on the metrics reported in the HTML file. Does anyone have any detailed explanation of these metrics? Specifically,

The #target regions metric seems to differ if I gave the same target regions file, but different bam files

Do the Coverage metrics refer to On-target reads only? And on a per-base or per-Amplicon basis? What exactly are the percentage reported?

Regards,

Mark

enrichment target • 2.2k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 6.4 years ago by mark.dunning200

is there an example of the output somewhere?

ADD REPLYlink written 6.4 years ago by Jeremy Leipzig17k

Have you tried asking the authors? The package does not seem to have documentation that includes that level of detail.

ADD REPLYlink written 6.4 years ago by Sean Davis25k
0
gravatar for mark.dunning
6.4 years ago by
mark.dunning200
The University of Sheffield
mark.dunning200 wrote:

Here is an example of the stats produced on the HTML page. I feel that some explanation would be useful

enter image description here

ADD COMMENTlink written 6.4 years ago by mark.dunning200

i speculate the covered metrics are almost certainly the fraction of the regions of interest covered at varying depths. "Covered 1x" makes no sense otherwise (how could on-target+off-target be anything but 100%)

ADD REPLYlink written 6.4 years ago by Jeremy Leipzig17k
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