SeqMap pipeline

SeqMap specifications

Information


Unique identifier OMICS_00684
Name SeqMap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTA, raw DNA sequence format
Output format Eland
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 1.0.13
Stability Stable
Source code URL http://www-personal.umich.edu/~jianghui/seqmap/download/seqmap-1.0.13-src.zip
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Hui Jiang <>
  • person_outline Wing Hung Wong <>

Publication for SeqMap

SeqMap citations

 (3)
2015
PMCID: 4467840

[…] analysis strategy’ and rnaseq data sets derived as described therein. these data were downloaded from the website http://chualab.rockefeller.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [11]., using seqmap [20], a. thaliana small interfering rna (sirna) data were mapped against transcripts of protein-coding genes, then secondly also against the transcripts of tair cis-nats, or (as appropriate) […]

2014
PMCID: 4254945

[…] the rpkm value was calculated based on the the number of reads mapping to each gene and the length of the gene [25]. a rpkm threshold value of 0.1 was set to detect the presence of a unigene. seqmap [26] was used for reads mapping and then rseq [27] was applied for rpkm based expression measurement. degs were identified by the deseq program [28]. genes with false discovery rates (fdr) […]

2014
PMCID: 4162972

[…] out as a custom service (beijing novogene bioinformatics technology co., ltd., beijing, china). the expression level of each assembled transcript in different samples was measured as rpkm values. seqmap [35] was used for read mapping and rseq [36] was applied for rpkm based expression measurement. abundance data from different samples were collected for each transcript. in our work, […]

SeqMap institution(s)
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA
SeqMap funding source(s)
National Institute of Health (R01HG003903 and U54GM62119).

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