ATAQV(1)

💖 NAME 💖

ataqv — QC metrics for ATAC-seq data, bestie. That's the whole vibe. 🧬✨

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🌸 DESCRIPTION 🌸

okay so. this is ataqv 1.3.1: QC metrics for ATAC-seq data. and it is so good at it. 💅

Here's how you run it:

ataqv [options] organism alignment-file

where, and I cannot stress this enough:

• organism is the subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" below, iykyk).
• alignment-file is a BAM file with duplicate reads marked. marked!! if you skipped that step, go back. 🚨

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✨ Basic options ✨

• --help — shows this usage message. classic. 🫶
• --verbose — shows more details and progress updates, so you can watch the little progress numbers do their thing. very satisfying ngl.
• --version — prints the version of the program. short and iconic.
• --threads <n> — the maximum number of threads to use (right now, only for calculating TSS enrichment). so like, it's giving parallel, but only for that one thing. 🔥

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🎀 Optional Input 🎀

• --peak-file "file name" — a BED file of peaks called for alignments in the BAM file. you can also say "auto" and it'll use the BAM file name with .peaks appended, or, if the BAM file contains read groups, it assumes each read group has a peak file whose name is the read group ID with .peaks appended. 👑

⚠️ and listen: if you specify a single filename instead of "auto" while you have read groups, the same peaks will be used for all reads. be sure this is what you want, bestie. no cap.

• --tss-file "file name" — 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. required. not optional. index it.
• --tss-extension "size" — if a TSS enrichment score is requested, it gets calculated for a region of "size" bases to either side of transcription start sites. the default is 1000bp. 💫
• --excluded-region-file "file name" — a BED file containing excluded regions. peaks or TSS overlapping these will be ignored. may be given multiple times, so stack 'em up. 🚫

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📊 Output 📊

• --metrics-file "file name" — the JSON file to which metrics will be written. the default filename will be based on the BAM file, with the suffix .ataqv.json. 💖
• --log-problematic-reads — 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. the problem children get their own little diary. 📓💀
• --less-redundant — if given, output a subset of metrics that should be less redundant. and heads up: if this flag is used, the same flag should be passed to mkarv when making the viewer. keep it consistent or the vibes get off. 🔁

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🏷️ Metadata 🏷️

the following options provide metadata to be included in the metrics JSON file. they make it easier to compare results in the ataqv web interface. so like, do it for the plot. 🫶

• --name "name" — a label to be used for the metrics when there are no read groups. if there are read groups, each will have its metrics named using its ID field. and with no read groups and no --name given, your metrics will be named after the alignment file. she names herself. 💅
• --ignore-read-groups — even if read groups are present in the BAM file, ignore them and combine metrics for all reads under a single sample and library named with the --name option. this also implies that a single peak file will be used for all reads; see the --peak option. 👀
• --nucleus-barcode-tag "nucleus_barcode_tag" — data is single-nucleus, with the barcode stored in this BAM tag. in this case, metrics will be collected per barcode. per barcode!! so many little guys. 🦋
• --description "description" — a short description of the experiment. keep it cute, keep it short.
• --url "URL" — a URL for more detail on the experiment (perhaps using a DOI). 🔗
• --library-description "description" — use this description for all libraries in the BAM file, instead of using the DS field from each read group. override energy. ⭐

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🧬 Reference Genome Configuration 🧬

ataqv includes lists of autosomes for several organisms, and here they all are, bestie:

• fly — 2R 2L 3R 3L 4
• human — 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
• mouse — 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
• rat — 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
• worm — I II III IV V
• yeast — I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI

the default autosomal reference lists contain names with "chr" prefixes (chr1) and without (1). the way that they gave us both?? so thoughtful honestly. 💜

if you need a different set of autosomes, you can supply a list with --autosomal-reference-file. ✨

• --autosomal-reference-file "file name" — 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. exactly. not "close enough". not "basically the same". exactly.
• --mitochondrial-reference-name "name" — if the reference name for mitochondrial DNA in your alignment file is not "chrM", use this option to supply the correct name. and again, if this name is wrong, all the measurements involving mitochondrial alignments will be wrong. 💀 so maybe double-check it. just a thought.

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and that's the whole page, bestie!! 🎀 you now know more about ataqv (version 1.3.1, from March 2026) than like 90% of people, fr fr. go forth and QC. you're gonna slay. 💅✨🦋🌈👑