Unverified Commit 2c14e3de authored by Li Song's avatar Li Song Committed by GitHub
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Update README.md

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@@ -113,9 +113,13 @@ threshold to make a correction by setting **--bc-probability-threshold**
corrections. For scATAC-seq data with multiple read and barcode files, you can
use "," to concatenate multiple input files as the example [above](#general). 

The BED format (fragment file) for bulk and single-cell are different except for the first
three columns. For bulk data, the columns are "chrom chrom_start chrom_end N mapq strand".
For single-cell data, the columns are "chrom chrom_start chrom_end barcode duplicate_count" 
The BED format (fragment file) for bulk and single-cell is different except for the first
three columns. For bulk data, the columns are

    chrom chrom_start chrom_end N mapq strand
For single-cell data, the columns are 
    
    chrom chrom_start chrom_end barcode duplicate_count
as the definition of the fragment file in 
[CellRanger](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments). 
Note that chrom_end is open-end.