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Noble-Lab / Polarbear

Polarbear translates between different single-cell data modalities
Apache License 2.0
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pre-processing of single-modality scATAC-seq data #1

Open hongruhu opened 2 years ago

hongruhu commented 2 years ago

Hi Dr. Zhang,

I read your Polarbear paper and planned to run the model on some multiomics data. It seems that the data provided via the link (https://noble.gs.washington.edu/~ranz0/Polarbear/data/) are pre-processed ones.

In the paper you mentioned that "because the ATAC-seq peak locations vary across datasets, we use the SNARE-seq peaks as a reference and map features from other datasets to SNARE-seq peaks if there is an overlap of 1 bp or more", and I was wondering if you mind providing the detailed information about the generation of the pre-processed data since I could not find the relevant code in this repo?

Thanks in advance for your time!

RanZhang08 commented 1 year ago

So sorry to have missed it! The overlap is calculated using bedtools, here's an example: bedtools intersect -a snareseq_peak.bed -b newdata_peak.bed -wa > intersect.bed Please let us know if there's any additional questions!