SeqPipe protocols

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SeqPipe specifications

Information


Unique identifier OMICS_01135
Name SeqPipe
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 0.4.17
Stability Stable
Requirements
GNU bash, GNU core utilities
Maintained Yes

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A C++ version is also available here: https://github.com/yanlinlin82/seqpipe/tree/cpp-v0.5

SeqPipe in pipeline

2016
PMCID: 4735512
PMID: 26759081
DOI: 10.1038/ncomms10291

[…] boundary for ubx or defining ‘near' as the 70 kb on one side of the viewpoint) with nearly identical results. for this analysis, the boundaries of the bx-c used were chr3r:12480479-12821577., 4c-seqpipe analysis was carried out as described. because our primers were designed to read second enzyme (dpnii) junction rather than the primary (nlaiii) one, dpnii was designated as the first cutter […]


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SeqPipe in publications

 (2)
PMCID: 4757527
PMID: 26886256
DOI: 10.1371/journal.pgen.1005840

[…] genome in k562 cells. in the gm12093 cells, 1,504,454 reads were obtained and 95.9% of them were successfully mapped. relative association with the vegfa promoter was analyzed with the use of the 4c-seqpipe tool []. for each cell type percent reads was calculated with 1-kb sliding widows at 50% overlap. the difference between the association of the esse site with the vegfa promoter in gm12093 […]

PMCID: 4735512
PMID: 26759081
DOI: 10.1038/ncomms10291

[…] ‘far' regions. we found that viewpoints in ph-ml cells have significantly decreased ‘far' interactions within the bx-c as compared with ph-wt cells (). we also analysed the 4c-seq data using the 4c-seqpipe software developed in the tanay lab and plotted interactions in the bx-c region. this analysis () is consistent with reduced interactions with sequences far from the viewpoint in ph-ml cells, […]


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