JIANHONG OU

If you sort the file correctly, this should not be a problem. Could you share me the bamfile to repeat your error? On Sun, May 5, 2019 at 8:40 PM...

I am trying to fix the bug. Please have a try with the newest development version.

Could you share the output of capabilities("cairo")

I don't think you will get gal1 if you did not get shifted bam file. Could you just try to sub sample your data to a small file by samtools...

Hi, Thank you for the comments. The memory and time cost is a big issue of ATACseqQC. Now I don’t have good solution for that. One Possible solution may split...

Hi josruirod, I improved the shiftGAlignmentsList function in the development version. Please have a try. Thank you.

May I know the seqlev you set?

Currently I fixed it by paste ^ and $ into exclude parameter of matchPWM. It will be release in bioconductor soon. Thank you for reporting the bug. Jianhong.

@hyjforesight Sorry for the late replay. I missed this email. Could you please share the minimized bam file to repeat your issue?

Thank you for reporting that. I will fix it as soon as possible.