Question

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

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13.4 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 • 6.0k views

ADD COMMENT • link updated 2.3 years ago by Ram 45k • written 13.4 years ago by Tianyang Li ▴ 500

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Did you try psl2sam.pl from this site?

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

ADD REPLY • link updated 6.0 years ago by Ram 45k • written 11.0 years ago by Manvendra Singh ★ 2.2k

score 1 · Answer 1 · 2012-07-02

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13.3 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 13.3 years ago by Zhidkov ▴ 600

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

ADD REPLY • link 11.8 years ago by Raymond301 ▴ 160

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ADD REPLY • link 9.2 years ago by jeltje.van.baren ▴ 80