Question

Convert A Psl File To A Sam File And Also Write Sequences To The Sam File?

1

Entering edit mode

10.9 years ago

Tianyang Li ▴ 500

Hi,

I'm wondering if there is an existing tool to convert a PSL file to a SAM file that also writes sequences to the SAM file?

I don't think __psl2sam.pl__ in __samtools__ could do it.

Thanks for your help!

sam convert • 4.9k views

ADD COMMENT • link updated 8.6 years ago by Biostar 20 • written 10.9 years ago by Tianyang Li ▴ 500

0

Entering edit mode

Did you try psl2sam.pl from this site?

they have modified psl2sam.pl codes which was originally from samtools

ADD REPLY • link updated 3.6 years ago by Ram 39k • written 8.6 years ago by Manvendra Singh ★ 2.2k

score 1 · Answer 1 · 2012-07-02

1

Entering edit mode

10.9 years ago

Zhidkov ▴ 600

Use BedTools to convert psl file to bed, then convert bed to bam, then with samtools bam to sam.

ADD COMMENT • link 10.9 years ago by Zhidkov ▴ 600

1

Entering edit mode

This isn't that useful....examples should be included.

ADD REPLY • link 9.3 years ago by Raymond301 ▴ 160

0

Entering edit mode

ADD REPLY • link 6.7 years ago by jeltje.van.baren ▴ 80