Sam to bowtie native format

Question

[druggable]

Hi everyone,

Does anyone know how to convert .sam files to the native bowtie format? I need this for peak calling using QuEST software for ChIP seq data.

Thanks a bunch!

teabonng

[GenoMax]

What is native bowtie format? Do you have a reference? If you are referring to the alignments written by bowtie then they are in SAM format, which is a standard.

[druggable]

Thanks for the replies, now I understand.

[ATpoint]

Just out of curiosity, why do you want to use an almost 10-year old peak caller?

Answer 1

[h.mon]

QuEST accepts sam files as inputs, which is Bowtie's output if you use the -S flag.

How to use QuEST for ATAC-Seq data

[ATpoint]

From this link:

For a 4.25 GB ATAC Sam file, it ran for 30 hours.

Well, this even more should motivate you to use a more recent peak caller. For ATAC-seq, I typically use MACS2:

macs2 callpeak -t file.bam -n samplename --nomodel -f BAMPE

It assumes that your file is paired-end.

[druggable]

Thank you so much for this.