bs_seeker2-align.py: pysam ERROR

[ruih-ruih]

@guoweilong
Dear Dr. Guo,

Hello! A few days ago, I reported an error about bam2cgmap of cgmaptools (guoweilong/cgmaptools#51). You suggested I can change BS-Seeker2 to align Bis-seq reads.
Recently, I downloaded BS-Seeker2-v2.1.8 and then aligned bis-seq reads with bs_seeker2-align.py. But the error information was reported : "[Error] It seems that you haven't install "pysam" package.. Please do it before you run this script."
After I downloaded the pysam-0.8.1 from github (https://github.com/pysam-developers/pysam/releases/tag/0.8.1) , the same error was still generated.
May I have your suggestions for this issue?
Thanks!

[BSSeeker]

It seems that you have not successfully installed the "pysam" package. Currently, it is recommended to use python2 (not python 3) and pysam v2.6 For pysam related issue, these Q&A might be useful. https://github.com/BSSeeker/BSseeker2#3-pysam-package-related-problem Best, Weilong At 2021-09-24 10:41:41, "xixiliangfengfeng" ***@***.***> wrote: @guoweilong Dear Dr. Guo, Hello! A few days ago, I reported an error about bam2cgmap of cgmaptools (guoweilong/cgmaptools#51). You suggested I can change BS-Seeker2 to align Bis-seq reads. Recently, I downloaded BS-Seeker2-v2.1.8 and aligned bis-seq reads with bs_seeker2-align.py. But the error information was reported : "[Error] It seems that you haven't install "pysam" package.. Please do it before you run this script." After I downloaded the pysam-0.8.1 from github (https://github.com/pysam-developers/pysam/releases/tag/0.8.1) , the same error was still generated. May I have your suggestions for this issue? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.