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pyCRAC specifications


Unique identifier OMICS_19144
Name pyCRAC
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Sander Granneman

Publication for pyCRAC

pyCRAC citations


An RNA dependent mechanism for transient expression of bacterial translocation filaments

Nucleic Acids Res
PMCID: 5909449
PMID: 29432565
DOI: 10.1093/nar/gky096
call_split See protocol

[…] in Tree et al. () and deposited at NCBI GEO under the accession number GSE46118. Raw sequence data was aligned to the EHEC str. Sakai genome (NC_002695.1) using novoalign software and analysed using pyCRAC software (). […]


RNA binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

BMC Biol
PMCID: 5678581
PMID: 29117863
DOI: 10.1186/s12915-017-0444-9

[…] in CLIP oligos) and amplified by PCR (P5_Forward and P3_barcode Reverse BC1 or BC2) using LA Takara Taq. The libraries were analyzed on an Illumina Miseq system, and the data were processed using the pyCRAC software []. TRIM25 binding motifs were analyzed using pyMotif and WebLogo on identified clusters. The distribution of TRIM25 CLIP clusters across the protein coding genes was performed using p […]


Binding to RNA regulates Set1 function

PMCID: 5654745
PMID: 29071121
DOI: 10.1038/celldisc.2017.40
call_split See protocol

[…] Clean-up, Macherey-Nagel, Düren, Germany) and sequenced using Illumina technology (San Diego, CA, USA). Primers are indicated in .Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite. Subsequently, the 3′ adaptor is clipped with Cutadapt and the resulting insert is quality trimmed from the 3′-end using Trimmomatic rolling mean clipping (window size=5, minimum […]


High throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast

Nat Commun
PMCID: 5620067
PMID: 28959008
DOI: 10.1038/s41467-017-00761-8

[…] l libraries were pooled based on concentration and barcoding, and paired-end sequencing was performed on HiSeq systems by Edinburgh Genomics (Edinburgh). Raw data processing was carried out using the pyCRAC software package and our ChemModSeq pipeline (see Data and code availability section below). Data from replicate experiments were summed to increase the total coverage. The ChemModSeqPipeline p […]


The N6 methyladenosine (m6A) forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells

Nat Med
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] escribed. In summary, raw miCLIP reads were trimmed of their 3′ adaptor and demultiplexed. Then, PCR-duplicated reads of identical sequences were removed using the script of the pyCRAC tool suite (version Unique reads were mapped with Novoalign (v3.02.12) using hg19 as reference genome. Further analysis including the identification of CITS was performed as previousl […]


The m6A pathway facilitates sex determination in Drosophila

Nat Commun
PMCID: 5500889
PMID: 28675155
DOI: 10.1038/ncomms15737

[…] flexbar -r read1.fastq -p read2.fastq -f i1.8 –a [adaptor sequences file] --pre-trim-phred 30 -n 20 -s –t [timepoint suffix]; and demultiplexed using from the pyCRAC software suite using the command: -f [timepoint suffix]_1.fastq -r [timepoint suffix]_2.fastq –b [barcode file]. PCR duplicates in the dataset were removed using pyFastqDupli […]


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pyCRAC institution(s)
Centre for Synthetic and Systems Biology (SynthSys), Kings Buildings, Edinburgh, UK; Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
pyCRAC funding source(s)
Supported by Wellcome Trust Research and Career Development Grants (097383, 091549), the Medical Research Council and the Wellcome Trust Centre for Cell Biology core grant (092076).

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