ATACorrect error: Peak region was removed at it is either out of bounds or not in the chromosomes given in genome/bam
kkohl96 opened this issue · comments
Hello,
I ran ATACorrect and got the following error for all the peaks in my bed file: "Peak region ('chr1', 911162, 911558, '', '.') was removed at it is either out of bounds or not in the chromosomes given in genome/bam".
Unfortunately, I couldn't figure out what the issue was since the peaks are also present in my bam file, I used the same genome (hg38) that was used for mapping and not only some, but all peaks gave the same error.
I would really appreciate your help if you ever experienced the same problem before or could think of a solution.
Thank you very much in advance!
Hi @kkohl96,
Yes, that indeed sounds a little strange - I didn't see that before. Is it possible for you to share the full log of the run with --verbosity 4 as parameter? That might write out a little bit more information which is helpful to see what is going on here, thank you!
Hi @msbentsen,
I solved the problem already, I used chr in front of the chromosome numbers and that didn't work.
Thanks for offering your help!
Do you know how to delete this post?
Great, thank you for the update! No need to delete it, I will just close it so that other people can see it for reference :-)