Extract 3'utr sequences from annotation file

Question

[SL]

Hi everyone, I have BAM files of two different conditions (KD vs CTR).

I would like to extract the 3´UTR from both files to see if the length in the KD condition over the control is affected. I know how to extract 3´UTR in WT with BiomaRt but how would I do that for my condition?

[iraun]

Not sure if I understand what is your goal. So, you want to know if the length of the 3'UTR has been affected, right? How would the length change? Due to some indel variant affecting the UTR? To check this, I would run a variant calling analysis, and extract the variants affecting your UTR, and see if there is any indel affecting the length of the UTR in the KD condition that is not present in CTR.

[SL]

I want to see if in my knockdown there is a processing defect hence, a longer or shorter 3´UTR.