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- person_outline Anshul Kundaje
Platelet function is modified by common sequence variation in megakaryocyte super enhancers
[…] 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
[…] 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
[…] 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
[…] 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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