Run with 10x scATAC data.

[YOU-k]

Hi there,
I am trying to run this pipeline with a scATAC-seq dataset generated with 10X chromium.
So, from my understanding based on the tutorial you provide, for -b, the R2 file should be the one to use which contains the information of the CBs. However, for the sequencing file R1, I am not quite sure where to put it.
Here is the code I used after indexing,
chromap --preset atac -x index -r $reference -1 ATACLib_S1_L001_R1_001.fastq.gz -o aln.bed -b ATACLib_S1_L001_R2_001.fastq.gz --barcode-whitelist $work_path/737K-cratac-v1.txt

However, I got an error like :
Start to map reads.
Parameters: error threshold: 8, min-num-seeds: 2, max-seed-frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 2000, MAPQ-threshold: 30, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90.

Is there any suggestion on how to make this work?

Cheers

[haowenz]

10X scATAC-seq data should be paired-end. You can input your the R3 from 10X using -2.

[YOU-k]

It works! Thanks.