Davide Cittaro

Hello, you can find example sequences [here](https://www.dropbox.com/s/ase45ltcc3b8xc6/seqs.tar?dl=0) I aligned to hg38 genome like this ``` chromap -r hg38.fa -x hg38.index -1 Sample_6_BC_AGGCTCCG_READ1.fq.gz -2 Sample_6_BC_AGGCTCCG_READ2.fq.gz --SAM -o test2.sam ```

> We just made an fix for the SAM format wich should resolve your issue of "Positional data too large". Excellent, I tried and everything seems to be solved, thanks...

If this option will be ever be implemented, it may be useful to allow output in .mtx format when analysing single cell data

I vote for exposing this feature + mtx output, there are some scATAC-seq analysis approaches which do not rely on fragments, for example [this](https://www.nature.com/articles/s41467-021-21583-9) and [this](https://f1000research.com/articles/9-199/v2).

Just checking… can you disclose which version of Chromap will enable this feature? Alternatively, can you hint how to expose it myself and give it a try?

My BED files are mostly fixed size bins, so I guess it will do the job! Thanks, I’ll spend some time in the following days to test it properly

Hello, I tried to expose this feature by uncommenting lines https://github.com/haowenz/chromap/blob/567fc3ed407dc577518b6ec779222d778f9eaf35/src/chromap.cc#L5941 to https://github.com/haowenz/chromap/blob/567fc3ed407dc577518b6ec779222d778f9eaf35/src/chromap.cc#L5950 but my output doesn’t seem to be binned, I have fragments resembling a ATAC output. I will...

Followup, I have a scATAC-seq with R1 and R3 to be mapped and cell barcodes in R2 (starting at position 9). The output of this ``` chromap -x GRCm38.index -r...

Thanks, I missed those lines. Anyhow, you were right, it doesn't work in the sense that ``` chromap -x GRCm38.index -r GRCm38.fa.gz \\ --low-mem -t 4 -1 READ1.fq.gz -2 READ3.fq.gz...

@joachimwolff thanks, my bad, I missed it, sorry. And yet, what is the rationale behind the +3,+4 shifting of the min_idx when concatenating the matrices?