metaseq statistics

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Associated diseases

Associated diseases

metaseq specifications


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


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

Additional information

Publication for metaseq

metaseq in publications

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

[…] 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 […]

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

[…] 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, (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, […]

PMCID: 3635150
PMID: 24964426
DOI: 10.1093/jscr/rjt015

[…] various-sized cylinders. then, based on the resulting numerical data, a 3-d image, which was converted by the surface-rendering technique, was reconstructed using software (metasequoia, (fig. c). when his virtual 3-d pulmonary model was reconstructed by cttry, the tumor was found to be involved in two subsegments [horizontal subsegment of apicoposterior segment (s1 + […]

PMCID: 2954202
PMID: 20944208
DOI: 10.1107/S1744309109022672

[…] 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, […]

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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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