Hi all,
I have ATAC-seq datas and I am trying to find TF binding motifs. I trimmed adapters(trim-galore), aligned to genome(with bowtie2), converted sam files to bam files and filtered them (according to mapping quality, duplicates and mitocondrial reads). Then, I wanted to look at my bam files. These are the results of "samtools idxstats"![enter image description here][1] command
chr1_KI270892v1_alt 162212 308 0
chr2_KI270894v1_alt 214158 1585 0
chr3_KI270895v1_alt 162896 540 0
chr6_GL000251v2_alt 4795265 10343 0
chr7_KI270899v1_alt 190869 942 0
I want to change those chromosome names with short names. Like this chr1_KI270892v1_alt -> chr1
How can I change all this names with short ones?
uh ? why would you want to do that ?
Because I have found a tool that can find TF activities between 2 conditions.But ıt only accepts chr1,chr2 ... format.
I am not sure how it uses chromosome names, but chr1_KI270892v1_alt is not the same thing as chr1. It would make as much sense to rename that as it would chr2 to chr1. While technically possible, it is not very meaningful.
You probably should use samtools (or another tool) to filter for just the relevant chromosomes.