sam/bam to bowtie

[maricu]

I have files in bam format of reads mapped with BWA, I would like to know if there's any tool available to convert to bowtie format. I have a program for downstream analysis (for the collapse of clones) which is written for bowtie format, hence I need to convert the bam into bowtie. I would very much appreciate any guidance here.

cheers,

M

[lh3]

you will lose gapped alignment and mapping quality produced by bwa, which may be useful to downstream analyses.

[maricu]

Hi,

The program I want to use removes clones an re calculates the quality string, I guess I can go back to sam once I know what reads are not clonal so I dont loose all the information. Alternatively I could ask if there is a way to remove clones in sam/bam output.
Thanks for your answer