Description

ataqv function of a corresponding ataqv tool

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM file

*.bam

bai (file)

BAM index file with the same prefix as bam file. Required if tss_file input is provided.

*.bam.bai

peak_file (file)

A BED file of peaks called for alignments in the BAM file

*.bed

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 (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

json (file)

The JSON file to which metrics will be written.

problems (file)

If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with “.problems” appended. If no read groups are found, the reads will be written to one file named after the BAM file.

*.problems

versions (file)

File containing software versions

versions.yml
included in
atacseq
maintainer
Github user i-pletenev
get in touch
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Tools

ataqv
GPL v3

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.

github.com/ParkerLab/ataqv/blob/master/README.rst https://github.com/ParkerLab/ataqv 10.1016/j.cels.2020.02.009