Question

How to convert a bam file into tsv file format?

0

Entering edit mode

malikbashirkhan2 • 0

@malikbashirkhan2-8918

Last seen 9.2 years ago

Pakistan

i have converted a sam file into bam. then sorted it and then indexed it .

now i just want to convert a this sorted, indexed file into tsv file format.

bioinformatics • 3.8k views

ADD COMMENT • link updated 9.2 years ago by Gordon Smyth 52k • written 9.2 years ago by malikbashirkhan2 • 0

0

Entering edit mode

What columns would you like in your tsv file?

ADD REPLY • link 9.2 years ago Martin Morgan 25k

0

Entering edit mode

i would like to convert a bam file completly into tsv file.

ADD REPLY • link 9.2 years ago malikbashirkhan2 • 0

1

Entering edit mode

But the SAM file you started with already contained all the information in tsv format. If it's small enough to fit into excel, just use excel to import it.

ADD REPLY • link 9.2 years ago Martin Morgan 25k

score 0 · Answer 1 · 2015-10-02

0

Entering edit mode

Gordon Smyth 52k

@gordon-smyth

Last seen 14 minutes ago

WEHI, Melbourne, Australia

It does seem that your queries have already been answered on Biostars:

https://www.biostars.org/p/160176/

https://www.biostars.org/p/160012/