converting Accepted_hits.bam to txt or bed

Question

[zizigolu]

Sorry friends,

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

Thank you

Answer 1

[Ashutosh Pandey]

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

[zizigolu]

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

[Ashutosh Pandey]

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

[zizigolu]

thank you Ashutos

Answer 2

[Alex Reynolds]

Another option is BEDOPS bam2bed:

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