Extract Specific RNA-seq reads from BAM using deeptools

Question

[Qilin]

Hello everyone,

I am working on RNA-Seq data analysis, and currently I have generated the bam files (named WT.bam and KO.bam).

Could I ask whether deeptools (https://github.com/deeptools/deepTools/) is available to extract reads that exist in WT.bam but not in KO.bam?

If it can't, is there any other methods (or scripts) to achieve the target?

Answer 1

[GenoMax]

to extract reads that exist in WT.bam but not in KO.bam?

Are you referring to recovering reads from areas of the genome that are covered in WT as opposed to the KO alignment file? If so, you could use bam2bed (https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/bam2bed.html ) to first convert the files and then use a set operation like difference (https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#difference-d-difference ).

Once you get the read names that are present in one of the files, you can use a tool like filterbyname.sh from BBMap suite to extract the reads from original files.