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Wiggler specifications


Unique identifier OMICS_29451
Name Wiggler
Alternative name align2rawsignal
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Anshul Kundaje

Wiggler citations


Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Nat Commun
PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] C-seq reads to GRCh37 using BWA and filtering of alignments (http://dcc.blueprint-epigenome.eu/#/md/dnase_seq_grch37) as well as for modelling fragment length with SPP and producing signal plots with align2rawsignal (http://dcc.blueprint-epigenome.eu/#/md/chip_seq_grch37) using the triweight smoothing method. Bedgraph files were converted to bigwig using bedGraphToBigWig (https://www.encodeproject […]


Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes

Nucleic Acids Res
PMCID: 4551926
PMID: 26150425
DOI: 10.1093/nar/gkv684

[…] g or unbinding ones. The ChIP-Seq, including TF binding and epigenomic signals, and processed RNA-Seq reads were downloaded from ENCODE (). The ChIP-Seq signals were uniformly normalized by using the align2rawsignal software (A. Kundaje, http://code.google.com/p/align2rawsignal/). When calculating Pearson correlation between AP and given annotation signal, the processed signal in the domain are su […]


Cancer associated ASXL1 mutations may act as gain of function mutations of the ASXL1–BAP1 complex

Nat Commun
PMCID: 4557297
PMID: 26095772
DOI: 10.1038/ncomms8307
call_split See protocol

[…] sing Bowtie (version 0.12.8), allowing only uniquely mapping reads, fragment sizes of 90–250 bp, and removing duplicates. Read density profiles were generated with WIGGLER ( https://code.google.com/p/align2rawsignal/). When calculating enrichments of areas around TSS, pseudo-count of 1 was added to both signal and input values. We employed a spatial clustering approach for identification of ChIP-e […]


Capture Hi C identifies the chromatin interactome of colorectal cancer risk loci

Nat Commun
PMCID: 4346635
PMID: 25695508
DOI: 10.1038/ncomms7178

[…] cell line HCT116 () were downloaded from ENCODE. Data consisting of replicates performed within and between different laboratories belonging to the ENCODE project were combined using WIGGLER (a.k.a. align2rawsignal). Read-shift parameters for ChIP-Seq data were calculated using PHANTOMPEAKQUALTOOLS. Using the ChromHMM software, genome-wide signal tracks were binarized (including input controls fo […]


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