NeMO atac-seq barcoding

Cell Taxonomies
1

Hello,
I’m interested in analyzing mouse snATAC-seq data posted on the NeMO data portal.
The compressed files contain read1 and read2 fastq files with what appears to be cell barcodes/UMIs in the fastq headers. However, I’m not sure which part of these headers are cell BCs/UMIs.
Is there a recommended way to align these files? I assume these data were generated via 10x sc-atac, but cellranger requires 4 files (1 genomic read pair and 1 index read pair).
Any guidance would be greatly appreciated.

Thanks,
Jesse

2

Hi Jesse,

I asked one of our team members to address this question and this is what they stated:
For the SMARTerV4 ATAC libraries, these will be paired end 50 fastq files from just a single nuclei (not 10X). This is the only ATAC data we have generated that would only have an R1 and R2 fastq file. I would suggest to use bwa to align this data.

Thank you

3

Thanks Susan, this answers my question. I appreciate it!