Convert A Psl File To A Sam File And Also Write Sequences To The Sam File?
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12.1 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 • 5.4k views
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Did you try psl2sam.pl from this site?

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

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12.1 years ago
Zhidkov ▴ 600

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

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

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