Maarten-vd-Sande
Maarten-vd-Sande
Just want to reiterate that compliant SAM would be nice :innocent:
Yes that works! :muscle: However I have a bit more complex setup with subparsers, and it does not work for the subparsers unfortunately :(
I am not sure if this is implemented. There are some flags for `UMI processing`, but I am not sure if they apply.
Yes that's also how I ended up fixing it! Thanks for actually putting the answer here :smile:
Yes when I worked with codeclimate i was struggling with this too. 5 is quite strict indeed. Maybe that number is based on different types of applications (not scientific code)?
In the end codeclimate is here to help you, not to limit you in your work
Seems that the lookup time just scales with the distance from the "start" of a contig. I just quickly scanned the internals, can't say I fully understand, but it _seems_...
@mdshw5 thanks for the reply, that makes sense! I guess I'll just load the whole fasta in memory for now :smile:
I have the same issue. In an earlier reply @r3fang replied that it is a Python issue (https://github.com/r3fang/SnapATAC/issues/80), but I have tried in both python 3 and 2.7, but it...
Sorry for reopening this discussion, but I have another question regarding ATAC-seq. I am interested in the cutting sites, so I want to use the --shift and --extsize options. However,...