Export meta.file like 10x cellranger

[BingjieZhang]

Hello,

First of all, thank you for developing chromap. It saves me tons of mapping time :) For a feature request, I am wondering if the chromap could generate sth like a summary report (at the cell level), just as the singlecell.csv file generated by 10x cellranger-atac. At least a duplication rate or saturation rate? Would be very useful for the library quality checks. Thanks again!

Best

[mourisl]

Thank you for the suggestion! We will implement this in the next version of Chromap. I think there is no definition of saturation rate in ATAC-seq, so we may not include it in the output.

[BingjieZhang]

Hi @mourisl first of all, Congratulations on your new Job!! I saw your announcement on Twitter lol Just wondering if you are still working on this....Or will you continue maintaining chromap in the future? My project now heavily relies on Chromap. Life would be much easier for me if it could export the metadata, especially peak_region_fragments... Anyway, thanks again for developing such a useful tool.

[mourisl]

Thank you, @BingjieZhang ! We are still actively maintaining Chromap. Thank you for this reminder and support of Chromap, and we will prioritize adding this feature. "peak_region_fragments" is after peak calling, so it will probably not be included in the output from Chromap.

[mourisl]

Hi @BingjieZhang, thank you for the reminder about this feature. I just implemented the option "--summary FILE_NAME" to output some mapping summary corresponding to the "barcode,total,duplicate,unmapped,lowmapq" columns in the singlecell.csv file from cellranger. The code is in the "li_dev4" branch on github. Could you please checkout this branch and give it a test?

The other fields in the singlecell.csv file requires peak calling or other annotations, which is beyond the scope of Chromap. But if you need some extra information solely from read mappings, please let us know.

Thank you.

[BingjieZhang]

Wow, thanks a lot. I really appreciated your help!

Ok, so I am sure I downloaded the right version, saw the help manual

      --barcode-translate FILE  Convert barcode to the specified sequences during output
      --summary FILE            Summarize the mapping metadata at bulk or barcode level

I passed the --summary parameter and no error message showed up. But I did not see the output of the summary file. Only the fragment file, the same as before?

[mourisl]

What was your full command?

[BingjieZhang]

/software/chromap-dev4/chromap --preset atac \
                   -x /hg38_chromap \
                   -r /fasta/genome.fa \
                   --remove-pcr-duplicates-at-cell-level \
                   --num-threads 10 \
                   --summary chromap-summary \
                   --bc-error-threshold 1 \
                   --read-format bc:0:15 \
                   -1 $name\_R1_001.fastq.gz \
                   -2 $name\_R3_001.fastq.gz \
                   --barcode $name\_R2_001.fastq.gz \
                   --max-insert-size 2000 \
                   --Tn5-shift \
                   --barcode-whitelist /R_whitelist.txt \
                   -o fragments.tsv

[mourisl]

I think I've found the issue. Could you please pull the li_dev4 branch again, and use "make clean; make" to recompile Chromap and give it a try? Thank you.

[BingjieZhang]

Thanks! It works well now! Exactly what I want to estimate the data quality.

[mourisl]

Great! We will update the documents, merge them into the master branch and release a new version soon. Thank you for the suggestions and tests.