Description

ataqv function of a corresponding ataqv tool

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

organism (string)

The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv).

mito_name (string)

Name of the mitochondrial sequence.

tss_file (file)

A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.

*.bed

excl_regs_file (file)

A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.

*.bed

autosom_ref_file (file)

A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

ataqv Documentation

ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.

https://github.com/ParkerLab/ataqvdoi: 10.1016/j.cels.2020.02.009License: GPL v3
Authors