Jeremy Simon comments

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                                            Jeremy Simon

Output peak by cell count matrix or mtx file

Hi @haowenz - I'm looking at using chromap in a similar fashion to the above. I have my chromap alignments for 4 samples, and I called peaks on each chromap...

Output peak by cell count matrix or mtx file

Thanks @haowenz. For others landing here, the MACS group seems to [recommend the following](https://github.com/liulab-dfci/MAESTRO/blob/master/MAESTRO/Snakemake/scATAC/rules/sc_atac_peak_call.smk) for peak-calling from the chromap fragments file, since they also are the authors of MAESTRO: ```...

Possible to add support for 10x VDJ?

Hey @rob-p , I know virtually nothing about this, but I've been having somewhat related discussions lately with @mourisl about their method TRUST4 (https://github.com/liulab-dfci/TRUST4) Li seemingly has interest in helping...

Does nf-core/atacseq apply an offset to each ATAC-seq fragment?

Now that v2.0 has come out, I'm curious if this was implemented yet? It seems pretty standard for ATACseq reads to be shifted in this way, such that `chromap` I...

Does nf-core/atacseq apply an offset to each ATAC-seq fragment?

Tagging @drpatelh - could we get an update on the above?

What types of mismatches are supported in `seqkit locate`?

Got it, thanks. And is there documentation on how the `MapQual` is calculated in `fish`? I think RawScore is based on the length of the query and the alignment parameters...

What types of mismatches are supported in `seqkit locate`?

Thanks @shenwei356 @botond-sipos that would be very helpful!

Clarification on how matches are determined within trackClonotypes?

Ah- my apologies, I think I missed a key difference in the output of say `MiXCR` vs that of `cellranger` in that `cellranger` only supplies one hit CDR3/V/J call for...

Translocations in alignment?

Would that be applicable even for scATAC-seq data? If so I can give it a try!