Hello,
is there a way to get an alignment file out? I am after something that you get after the tview command but I want it in a text file.
Is there a way to do this?
Thank you
PS: I cannot reply to Pierre. This doesnt work for me and produces something like this:
CG************C***********
S. .
TC************.***********
.C************G***********
TT************G***********
I dont seem to be able to reply or add comments. I am using the latest version.
I suppose you're asking about samtools tview , use option '-d '?
$ samtools tview -d T -p ref:20 --reference toy.fa toy.bam > align.txt
$ cat align.txt
21 31 41 51 61 71 81
CTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.....K.K......K. ..........
... ,,,,, ,,,,,,,,,
..>>>>>>>>>>>>>>T.....
Hi, unfortunately this doesnt work for me. Any idea? My goal is to look at correlated mutations in particular reads. Wanted to extract reads that cover both of these mutations using python from the raw alignment file. Do you have any other idea how to do that?
Hi, unfortunately this doesnt work for me
without any error message / command it's not possible to help you.
Wanted to extract reads that cover both of these mutations using python from the raw alignment file.
how is it related to your initial question ?
I dont get an error message but this what I get back:
CG************C*********** S. .
TC************.*********** .C************G*********** TT************G***********
Its not in the nice readable format you show. My command - samtools tview -d T s90_mapped-sorted.bam ref_E2_J6.fa > align.txt
•
written
by
vellryba •
what's your version of samtools ?
My samtools are version v.1.8
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Which version of
samtoolsare you using? Hopefully the latest (v.1.8).