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piPipes specifications

Information


Unique identifier OMICS_06048
Name piPipes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl, Python, R, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for piPipes

piPipes in publications

 (6)
PMCID: 5836094
PMID: 29444933
DOI: 10.15252/embr.201744957

[…] small rna‐sequencing by hiseq from e16.5 and post‐natal day 24 testes were described elsewhere . for paired‐end libraries, only perfectly complementary paired reads were extracted for analysis. pipipes was utilized for small rna‐sequencing analysis . the parameters used were as follows: zero mismatches allowed for ribosomal rna mapping, hairpin mapping, and genome mapping; and up to two […]

PMCID: 5678422
PMID: 29100015
DOI: 10.1016/j.stem.2017.10.004

[…] assembly using bowtie2. raw overlap counts for each small rna molecule were quantitated using seqmonk. graphing and statistics was performed using excel or r. for consensus sequence mapping the pipipes small rna pipeline was used (https://github.com/bowhan/pipipes) (). iapez consensus sequences were used from repeatmasker libraries (repeatmasker v4.0.3, library version 20130422). […]

PMCID: 5383398
PMID: 28384097
DOI: 10.7554/eLife.24695.029

[…] by repeatmasker from the vertebrate archive repbase. the final total set of 200 te families and their corresponding names in repbase and repeatmasker are listed in ., analyses were performed using pipipes v1.4 (). all data from the small rna-seq, ribosome profiling, rna-seq, and genome sequencing were analyzed using the latest chicken genome release galgal5 (gca_000002315.3). generally, one […]

PMCID: 5324852
PMID: 27929729
DOI: 10.1080/15548627.2016.1261319

[…] at least 2 counts per million mapped reads were considered for quantification analysis. tmm normalization was applied to account for the compositional bias. transposons were quantified using the pipipes pipeline that uses the repbase database for the transposon sequence information. cufflinks and cuffmerge (version 2.1.1) were used to predict novel intergenic transcripts. individual counts […]

PMCID: 5064768
PMID: 27728778
DOI: 10.1016/j.devcel.2016.09.015

[…] sequencing of all libraries was carried out with single-end protocols on a hiseq 2000 instrument (illumina)., smrna-seq data processing was performed using the freely available pirna pipeline pipipes (https://github.com/bowhan/pipipes) (). smrna-seq libraries were trimmed to remove poor-quality reads, adapters, and barcode sequences. trimmed data were mapped using bowtie against the mm9 […]


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piPipes institution(s)
RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA

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