Compatibility with old snap files generated from SnapTools

[AprilYuge]

Hi,

I downloaded some snap files from this url https://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/ATACseq/mouse/processed/analysis/EckerRen_Mouse_MOp_methylation_ATAC/dataset/ATAC/ and I was wondering if there is a way to extract fragment files from these snap files?

Thank you in advance!

[yal054]

You can extract reads by using a function called "dump-fragment" from Snaptools (https://github.com/r3fang/SnapTools).
usage: snaptools dump-fragment --snap-file {input.snap} --output-file {output.bed}

I recommend you to direct to our web portal: http://catlas.org, where you can find the fragment files directly from this link: http://catlas.org/mousebrain/#!/downloads

[AprilYuge]

Thank you for the reply! The web portal is really a valuable resource, but the last link doesn't seem to point me to the the same study (https://www.nature.com/articles/s41586-021-03500-8).

[yal054]

Thank you for the reply! The web portal is really a valuable resource, but the last link doesn't seem to point me to the the same study (https://www.nature.com/articles/s41586-021-03500-8).

In the study you mentioned, they actually only used a subset of samples (from primary motor cortex). You can find those samples from the link I provided, as well as samples from other brain regions.

[AprilYuge]

Do you mean that I can find the same set of cells in both studies?

[yal054]

Do you mean that I can find the same set of cells in both studies?

Yes exactly, you can match them by checking the sample names (e.g. CEMBA171206_3C) and cell barcodes.

[AprilYuge]

I see, thx!