Haowen Zhang

Did you try "--output-mappings-not-in-whitelist" with "k17 w7" and get low mapping rate? Or you can just remove "-b" and run your data as bulk ATAC-seq data and see if the...

@mourisl I think we should add a new mapping stats saying the number of reads skipped since their barcodes are not on the whitelist. This would help the users and...

Thank you so much for the suggestions! They make a lot of sense. Li and I will take care of this.

As two Hi-C reads in a pair are usually aligned to positions that are far away on the reference genome, you have to use "--TagAlign", which allows you to output...

Sorry for the late reply. You are right. It seems that there are just too many reads. We will try to fix this soon. Thanks for trying the tool.

We actually have this implemented but not made available to users for now. We may include this feature in the future release. For now you might be able to get...

Hi, I checked the code and found out that currently Chromap can only generate cell-by-bin matrix with fixed bin sizes instead of taking a BED file that contains the intervals...

Thanks for trying. You also have to uncomment these two lines: https://github.com/haowenz/chromap/blob/567fc3ed407dc577518b6ec779222d778f9eaf35/src/chromap.cc#L5968-L5969 And set this parameter to a name prefix you desire, there will be several files generated with that...

I guess that might just be a wrong log output. Can you share the whole log file with us? And can you provide more details about your data? What is...

Sorry for the late reply. From the log file, it is hard to tell the reason. It might be easier if you can share a sample of your reads and...