No scATAC barcodes found using v0.1.5

[timoast]

I'm mapping some scATAC-seq data using chromap with the following command:

chromap --preset atac \
          -x hg38.fna.chromap \
          -r  hg38.fna.gz \
          -1 scATAC_R1.fastq.gz \
          -2 scATAC_R3.fastq.gz \
          -o mapped/sample.bed \
          -b scATAC_R2.fastq.gz \
          --barcode-whitelist data/737K-cratac-v1_revcomp.txt \
          --read-format bc:15:-1 \
          -t 6

After updating to v0.1.5 I get the following error: Less than 5% barcodes can be found or corrected based on the barcode whitelist. Downgrading back to 0.1.3 (what I used previously) with the same command runs without error.

[haowenz]

This is a new feature introduced by @mourisl. Basically it warns the user when <5% of the input barcodes are in the whitelist and stops the mapping. Does the mapping stats make sense for Chromap v0.1.3? I mean most of the reads are mapped? And are you sure that the input barcodes R2 are mostly in the whitelist? If you are sure about this, you can use --skip-barcode-check to skip this check.

[haowenz]

Your command line also seems not correct --read-format bc:15:-1 means the barcodes start from 15th position and end at its end of each read in the barcode file scATAC_R2.fastq.gz. Not sure if this is what you want.

[timoast]

Hi @haowenz

I'll have to double-check what the alignment rate was using 0.1.3 and get back to you on that. These reads were quite noisy, so it's possible the rate was low.

Your command line also seems not correct --read-format bc:15:-1 means the barcodes start from 15th position and end at its end of each read in the barcode file scATAC_R2.fastq.gz

Yes, this is what I need for my sequencing format

[mourisl]

@timoast Sorry for the delayed reply. I just fixed the bug, could you please try the github branch "custom_readformat" for this?

[timoast]

Hi @mourisl, I just tried the new version and it works great! No longer see the error about low % barcodes, and get many more fragments in the output. Thanks!