Genomedata protocols

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Genomedata specifications

Information


Unique identifier OMICS_02148
Name Genomedata
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes

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Publication for Genomedata

Genomedata in pipeline

2009
PMCID: 2636879
PMID: 19204800
DOI: 10.1371/journal.pone.0004429

[…] putative genes for which the p value was less than 0.05 were considered as differentially expressed., gene annotations in the tables were based on an initial search of tgd (http://www.ciliate.org/genomedata.shtml) with the gene id indicated by the roche-nimblegen array design. if a hit to a gene of known function was obtained, the annotation was used (e value is “0.0”). if a hit […]


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Genomedata in publications

 (12)
PMCID: 5429002
PMID: 28338822
DOI: 10.1093/jxb/erx010

[…] analysing the rna-seq data (deposited in ncbi sequence read archive (sra) database with bioproject id prjna354681). the reads were mapped on the pigeonpea genome (; http://www.icrisat.org/gt-bt/iipg/genomedata.zip) using a splice-aware alignment algorithm, tophat (v 2.1.0) (). thereafter, the mapped reads were assembled into transcripts and their abundances were estimated using cufflinks (v […]

PMCID: 5259786
PMID: 28117353
DOI: 10.1038/srep41061

[…] analysis of global expression changes and ontology network assessment on the 2445 differentially selected genes was performed using mathematica® v10. ontology groups were generated using inbuilt genomedata, matching the annotated genes with pre-defined processes and intracellular functions. ontological information for gene processes was found for 1660 genes matching 1446 processes. two […]

PMCID: 5137433
PMID: 27587586
DOI: 10.1093/nar/gkw760

[…] sequence tag enrichment was then detected using sicer (v1.1, http://www.ncbi.nlm.nih.gov/pubmed/19505939). in order to be able to process data aligned to grch37 with this algorithm the genomedata class had to be amended accordingly. the wrapper shell scripts have been amended, so that several instances of the program could be executed in parallel. sicer was then run […]

PMCID: 5054876
PMID: 26397045
DOI: 10.1111/pbi.12470

[…] incidence score from 0% to 100% for fw and 0% to 100% for smd., icpl 20096 short reads were aligned to the publicly available pigeonpea genome of asha (icpl 87119) (http://www.icrisat.org/gt-bt/iipg/genomedata.zip)., parents and bulks used for seq‐bsa analysis., parents and bulks used for nonsynonymous snp (nssnps) analysis., parents used for expression profiling studies., parents and bulks used […]

PMCID: 4482647
PMID: 26114291
DOI: 10.1371/journal.pone.0129016

[…] mays) []., the following genomes were obtained from other sources: kiwifruit (actinidia chinensis) [], sugar beet (beta vulgaris) []; pigeonpea (cajanus cajan) [] http://www.icrisat.org/gt-bt/iipg/genomedata.zip; pepper (capsicum annuum) []; chickpea (cicer arietinum) [] http://www.icrisat.org/gt-bt/icggc/genomedata.zip; lotus japonicus [] ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/; banana […]


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Genomedata institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
Genomedata funding source(s)
Supported by National Institutes of Health (HG004695).

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