converting multiple bam files to bed

Bedtools – converting multiple bam files to bed

1

Hi all,

I have previous experience in R, but since some months ago I am trying new things in Python (JupyterLab).

I have a a directory with different files. Some of them are ‘.bam’ files. My objective is to obtain ‘.bed’ files from them. Therefore, I start as follows:

from pybedtools import BedTool
import os, fnmatch
bam_files = fnmatch.filter(os.listdir(‘.’), ‘*.BAM’) #To filter only ‘.bam’ files in working directory file

After this, I try to work with the expression

bedtools bamtobed -i reads.bam > reads.bed

But I think, as I have multiple files, I am doing something wrong. Any help about how to proceed to convert my multiple files??

Thank you very much!!


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Bedtools


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