Question: Is There A Way To See An Alignment In A Text File?
2
gravatar for diltsjeri
8.2 years ago by
diltsjeri440
Chicago, IL
diltsjeri440 wrote:

I know I can view a BAM in IGV, but I'm interested in working with a text file. Is there a way to see an alignment in a text file?

Thanks!

alignment text file • 3.1k views
ADD COMMENTlink written 8.2 years ago by diltsjeri440
4
gravatar for Pierre Lindenbaum
8.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

use samtools tview http://samtools.sourceforge.net/samtools.shtml

I also wrote a standalone/streaming version http://plindenbaum.blogspot.com/2011/07/text-alignment-viewer-using-samtools.html

ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Pierre Lindenbaum130k

Thanks. I will give it a try.

ADD REPLYlink written 8.2 years ago by diltsjeri440

I second this. For viewing alignments quickly and simply, samtools tview provides everything you need.

ADD REPLYlink written 8.2 years ago by Matt Shirley9.4k
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