How to make bam from start pos of read 1 and end pos of read 2 from paired end bam files

Question

[genomics_student]

Hi! I have a paired end bam file and used bedtools to convert it to bed format (paired end). From this bed file I want to make a new bam file from the start pos of read 1 and end pos of read 2. I already tried using bedtools bed to bam (using mouse genome file) but it seems that the output is incorrect. Thanks!

[Pierre Lindenbaum]

it is difficult to understand. Please explain better.

[Pierre Lindenbaum]

please, validate or comment all your previous questions: How to Analyze Overlapping Peaks of ChIP-Seq Data using Perl Programming Perl Programming - How to join two columns of a text file, in which values of the first column should match in order with the values of the second column

[cmdcolin]

you may want to explain what your goal is by doing this transformation, because ultimately, this proposed data transformation is "odd", and knowing your aim may help to get you on the right path (see https://xyproblem.info/)