Haowen Zhang

> Thank you for the updation. I tried with the v0.2.2 and the distribution of fragment length is correct now. > > However, the fragments with length 0 still exist....

Thanks for trying out and providing all the information for us to debug this! We were able to reproduce the error. We didn't perform many tests on this kind of...

The issue is caused by adapter trimming in this case. Since the adapters already have been trimmed for this dataset, the lengths of reads are various. This caused some problem...

Sorry for the long wait. This issue is now fixed in v0.2.2. Feel free to try the new version.

1. Currently, Chromap doesn't check restriction enzyme motif at the clip sites. We plan to add this feature in the future. 2. You should at least dedup using pairtools, which...

Did you try to run Chromap without `--skip-barcode-check`? As you are running Chromap to map paired-end reads (you use `-1` and `-2`), it seems that the number of reads in...

What do you mean by scores and strands?

To my knowledge, the fragment files generated by Cellranger and used by downstream analysis tools follow the current output format (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments) without mapq and strand. Could you tell which tool...

Thanks for testing. For us to reproduce the problem, can you share the test data and the command lines you used to run Chromap?

I know SAM is perhaps still the format that is used most of the times. But SAM file is large and would be slow to generate. That's why Chromap tries...