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

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
• 6,264 views • link
updated by Ram Ram • written by Tianyang Li • Tianyang Li

Did you try psl2sam.pl from this site?

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

• 0 views • link
updated by Ram Ram • written by Manvendra Singh Manvendra Singh

1 answer

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

• 0 views • link
written by Zhidkov Zhidkov

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

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written by Raymond301 • Raymond301

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