PARpipe specifications

Information


Unique identifier OMICS_28111
Name PARpipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A demultiplexed PAR-CLIP library.
Input format FASTQ
Output data A file of compressed SAM file with genomic alignments, sorted indices, clusters locations, statistics for found clusters, summary information, the distribution, gene-level information, statistics for each found group, PARalyzer parameters and binding behaviour by annotation categories.
Output format SAM+BAM+BED+CSV+TXT+CSV+CSV+PDF
Operating system Unix/Linux
Programming languages Perl, Python, R, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
Bpipe, Bowtie, SAMtools, BEDtools, cutadapt
Maintained Yes

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Versioning


No version available

Documentation


Additional information


https://ohlerlab.mdc-berlin.de/software/PARpipe_119/

PARpipe citation

library_books

An RRM–ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

2017
Nucleic Acids Res
PMCID: 5499739
PMID: 28379442
DOI: 10.1093/nar/gkx225

[…] d PAR-CLIP data () were downloaded from NCBI GEO database (Accession number: GSE44976). Analysis of alternative splicing was done using ExpressionPlot pipeline (). PAR-CLIP reads were processed using PARpipe pipeline (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/) based on the PARalyzer tool (). Two replicates were processed separately and only clusters with the T-to-C conversion >0.95 pres […]

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