Protocols

AQUAS specifications

Information


Unique identifier OMICS_24442
Name AQUAS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.3.3
Stability Stable
Source code URL https://codeload.github.com/kundajelab/chipseq_pipeline/tar.gz/0.3.3
Maintained No

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AQUAS citations

 (2)
call_split

Endothelial deletion of Ino80 disrupts coronary angiogenesis and causes congenital heart disease

2018
Nat Commun
PMCID: 5785521
PMID: 29371594
DOI: 10.1038/s41467-017-02796-3
call_split See protocol

[…] ds were programmatically downloaded with Aspera ascp executable (v.3.5.6) and converted to Fastq with fastq-dump (v.2.5.7). ChIP-seq coverage tracks were generated from raw sequencing reads using the AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline). Briefly, reads were aligned to Mus musculus genome assembly mm10 (for consistency with RNA-seq) using BWA, de-d […]

call_split

Multiscale 3D Genome Rewiring during Mouse Neural Development

2017
Cell
PMCID: 5651218
PMID: 29053968
DOI: 10.1016/j.cell.2017.09.043
call_split See protocol

[…] of mapped reads (RPM) in 10bp bins.To determine the peaks for ChIPs with narrow binding profiles (CTCF, Ring1B, H3K4me3, H3K27ac, Pax6, NeuroD2 and Tbr1), datasets were uniformly processed using the AQUAS Transcription Factor pipeline (based off the Encode (phase-3) specifications) with default parameters (IDR = 5%). Peaks for Nanog, ES_H3K4me3 and ES_H3K27ac were downloaded directly from the ENC […]

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