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3 hours ago by

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?

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