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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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bed file format for ATAC-seq integration #184

Closed PeterZZQ closed 3 years ago

PeterZZQ commented 4 years ago

Hi,

I just tried to run through your scATAC-seq and scRNA-seq integration manuscript. Can you pls provide the hg19_genes.bed and hg19_promoters.bed file. I downloaded the hg19_genes file from BioMart and generate the bed file as chrx-start-end form, and generate promoter using 3000bp upstream, i.e. chrx-(start-3000)-start, but after going through the pipeline, I only have 4 columns, which is basically like this:

image

And then I run into error when applying makeFeatureMatrix function, since I don't have column 7.

skpalan commented 3 years ago

Hi, the index files should contain 6 columns. For details, you can refer to the actual files (hg19_genes.bed and hg19_promoters.bed) we used in the tutorial here.