ATACorrect not work with different versions

Hi, developers: Thanks for developing this excellent package for ATAC-seq footprinting. This package is powerful and seamless across different steps. However, recently I found the ATACorrect not works when I update the version from 0.8.0 to 0.12.0 and 0.12.6.

In the 0.8.0 version, I successfully corrected my bam file and the log information suggested the post-bias variance reduced significantly than the pre-bias variance.

However, in the 0.12.0 and 0.12.6 version, it seems the correction failed, when I used exactly the same input file and parameter for the ATACorrect. I only show result from the 0.12.6 version here:

The command line I used is: TOBIAS ATACorrect --bam Human_K562_rep1.bam --genome Homo_sapiens.GRCh38.dna.primary_assembly.fa --peaks peaks.bed --blacklist hg38-blacklist.v2.bed --outdir ./ --cores 30

I don’t know whether the command lines or any parameters changed among these versions, which caused this inconsistency. Thanks in advance for your reply!

Best Wishes, Houyu.

[HouyuZhang]

Thanks for your reply, Mette.

You have already perfectly answered all my questions, and I have no more questions now. I will continue to use your excellent package in future studies. Thanks again for all!

Best wishes, Houyu.

[HouyuZhang]

Hi, Mette, Thank you for releasing the 0.8.1 version, it works well on my data, it seems the correction was much better than version 0.8.0:

Thanks again for your time and help! Best wishes, Houyu.