pyCRAC protocols

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pyCRAC specifications

Information


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
Version 1.2.2.9
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sander Granneman <>

Publication for pyCRAC

pyCRAC in pipelines

 (8)
2017
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 pybarcodefilter.py from the pycrac software suite using the command: pybarcodefilter.py -f [timepoint suffix]_1.fastq -r [timepoint suffix]_2.fastq –b [barcode file]. pcr duplicates in the dataset were removed using […]

2017
PMCID: 5500899
PMID: 28748221
DOI: 10.21956/wellcomeopenres.11564.r23177

[…] 8 and 12 nt, considered as “short reads” were selected and processed separately in downstream analyses., counting overlaps with features and prioritization. downstream analyses were performed using pycrac software ( ). to count overlaps with genes and reads per millions per kilobase (rpkm), pyreadcounters (pycrac package) was used. substantial numbers of short reads were aligned to antisense […]

2017
PMCID: 5620067
PMID: 28959008
DOI: 10.1038/s41467-017-00761-8

[…] script., the chemmodseq pipeline first trims the adapter sequences from the reads using flexbar followed by demultiplexing of the samples using pybarcodefilter from the pycrac package. this removed the barcode information in the forward reads except for the last random nucleotide, which was removed using the trimnucs.py script. the random barcode information (seven […]

2017
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] in summary, raw miclip reads were trimmed of their 3′ adaptor and demultiplexed. then, pcr-duplicated reads of identical sequences were removed using the pyduplicateremover.py script of the pycrac tool suite (version 1.2.2.3). unique reads were mapped with novoalign (v3.02.12) using hg19 as reference genome. further analysis including the identification of cits was performed […]

2016
PMCID: 4915518
PMID: 27288397
DOI: 10.15252/msb.20166869

[…] using fastx‐clipper to remove the 3′‐linker sequence and quality‐filtered using fastq_quality_trimmer (‐t 30) and fastq_quality_filter (‐q 23 ‐p 100). preprocessed reads were demultiplexed using pycrac (webb et al, ) and index and random barcode sequences from the 5′ ends of reads were removed. reads were mapped to the yeast genome (saccer3, downloaded from the saccharomyces genome database) […]


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pyCRAC in publications

 (28)
PMCID: 5909449
PMID: 29432565
DOI: 10.1093/nar/gky096

[…] 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 ()., rnas that interact with hfq were identified under conditions known to promote t3s expression in e. coli o157:h7 strains (growth in mem-hepes medium). hfq uv-crosslinking (crac) […]

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

[…] interactions (data not shown). the rna from the t7-trim25/rna complex was isolated using a clip-seq protocol and sequenced on a hiseq platform. data analysis and cluster identification using pycrac [] revealed a significant correlation between three biological replicates, with a correlation coefficient between clusters from 0.94 to 0.96 (additional file : figure s4). a total of 5549 […]

PMCID: 5654745
PMID: 29071121
DOI: 10.1038/celldisc.2017.40

[…] 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 […]

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

[…] 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 […]

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 pybarcodefilter.py from the pycrac software suite using the command: pybarcodefilter.py -f [timepoint suffix]_1.fastq -r [timepoint suffix]_2.fastq –b [barcode file]. pcr duplicates in the dataset were removed using […]


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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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