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metaseq specifications

Information


Unique identifier OMICS_09785
Name metaseq
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format BAM,bigBED,bigWIG,BED,GFF,GTF,VCF
Operating system Unix/Linux, Mac OS
Programming languages Python, R, Shell (Bash)
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Ryan K. Dale
  • person_outline Elissa P. Lei

Additional information


https://daler.github.io/metaseq/index.html#

Publication for metaseq

metaseq citations

 (4)
library_books

Genome wide characterization of human L1 antisense promoter driven transcripts

2016
BMC Genomics
PMCID: 4908685
PMID: 27301971
DOI: 10.1186/s12864-016-2800-5

[…] cells, we also downloaded alignments for YY1 ChIP-seq data and input controls. The average ChIP enrichment of EST TSS for plus- and minus-strand L1 ASP transcripts was calculated using Python package Metaseq using a genomic window of +/−1000 bp TSS and a 100 bp bin size to calculate depth []. The results for the plus and minus strands were merged, where −1000 bp represented upstream of the TSS and […]

library_books

Dynamics in Transcriptomics: Advancements in RNA seq Time Course and Downstream Analysis

2015
Comput Struct Biotechnol J
PMCID: 4564389
PMID: 26430493
DOI: 10.1016/j.csbj.2015.08.004

[…] ChIP-seq data (e.g: ChIP Array , EMBER for static experiments, and for TC experiments ). Up to date, there are several multi-stage tools available to analyze RNA-seq and ChIP-seq, e.g. INsPeCT and metaseq , but only few integrated meta-dimensional approaches e.g. Beta , CMGRN and Ismara . Nevertheless, none of the mentioned methods offer specific TC algorithms for analysis, and most tools eith […]

library_books

Binocular stereo navigation for three dimensional thoracoscopic lung resection

2015
PMCID: 4427933
PMID: 25952998
DOI: 10.1186/s12893-015-0044-y

[…] he pulmonary vessels and bronchi were rendered various sizes of cylinders. In accordance with the resulting numerical data, a 3-D image was reconstructed by Metasequoia shareware (Metasequoia, http://metaseq.net/) (Fig. ). Subsequently, the data of the reconstructed 3-D images by Metasequoia were converted to Autodesk data with Autodesk® 3ds Max® 2012 (Autodesk, San Rafael, CA, USA). Finally, REMO […]

library_books

The structure of the first representative of Pfam family PF09836 reveals a two domain organization and suggests involvement in transcriptional regulation

2009
PMCID: 2954202
PMID: 20944208
DOI: 10.1107/S1744309109022672

[…] 216 proteins from 173 species (170 from proteobacteria and one each from acidobacteria, bacteroidetes and planctomycetes). Pfam also indicates that this domain is observed in 68 sequences from NCBI’s METASEQ metagenomics data set. Of these 216 proteins, 215 have a single N-terminal DUF2063 domain and, in one instance, this domain is found with a DUF692 domain (PF05114; TIM barrel superfamily, Pfam […]

Citations

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metaseq institution(s)
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
metaseq funding source(s)
Supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases (DK015602-07).

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