converting Accepted_hits.bam to txt or bed

Sorry friends,

How can I convert the accepted_hits.bam produced by tophat to txt and bed?

Thank you

bam bed

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updated 3.9 years ago by Ram

• written 10.9 years ago by zizigolu

2 answers

http://bedtools.readthedocs.org/en/latest/content/tools/bamtobed.html

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written 10.9 years ago by Ashutosh Pandey

Sorry the accepted_hits.bam produced by tophat is the same normal bam which can be converted by bedtools to bed file?

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updated 3.9 years ago by Ram

• written 10.9 years ago by zizigolu

Honestly speaking I have never tried it but I see no reason why it won't work with bedtools.

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written 10.9 years ago by Ashutosh Pandey

thank you Ashutos

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written 10.9 years ago by zizigolu

Another option is BEDOPS bam2bed:

http://bedops.readthedocs.org/en/latest/content/reference/file-management/conversion/bam2bed.html

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written 10.9 years ago by Alex Reynolds

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