Question: Mean coverage in Ion Torrent PGM
0
gravatar for Abdul Rafay Khan
4 days ago by
Karachi, PK
Abdul Rafay Khan740 wrote:

Is there any way to calculate the mean coverage of each amplicon in a whole run (in 16 or 32 samples)?

coverage ngs ion torrent • 68 views
ADD COMMENTlink modified 4 days ago by haro220 • written 4 days ago by Abdul Rafay Khan740
1
gravatar for haro
4 days ago by
haro220
France
haro220 wrote:

Hi Abdul Rafay Khan,

You can use samtools depth:

samtools depth -b file.bed -a file.bam > coverage.csv

Also, a plugin named 'coverageAnalysis' exists directly on the Proton machine

ADD COMMENTlink modified 4 days ago • written 4 days ago by haro220
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