EMSAR statistics

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EMSAR specifications

Information


Unique identifier OMICS_09834
Name EMSAR
Alternative name Estimation by Mappability-based Segmentation And Reclustering
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An alignment file (SAM, BAM and default Bowtie1 output format) and a transcriptome FASTA file as input.
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Peter J. Park <>

Publication for Estimation by Mappability-based Segmentation And Reclustering

EMSAR in publications

 (2)
PMCID: 5428675
PMID: 28377623
DOI: 10.1038/s41598-017-00534-9

[…] bio-phmshfrs, pflhdc, phmshfrs and their unrelated fragments (urds) were amplified from the genomic dna of ypiii, with primers flhdc-biotinf/flhdc-biotinr, hms-biotinf/hms-biotinr, flhdc-emsaf/flhdc-emsar, hms-emsaf/hms-emsar, flhdc-urd f/flhdc-urd r, and hms-urd f/hms-urd r, respectively. all pcr fragments were purified by easypure quick gel extraction kit (transgen biotech, beijing, china). […]

PMCID: 4847940
PMID: 26501951
DOI: 10.1038/nbt.3388

[…] from ensembl (grch37.67) reference chromosomes, then entries with identical gene symbols were merged. the transcriptome includes both protein-coding genes and non-coding genes such as lincrnas. emsar was used to quantify the expression levels in tpm (transcripts per million) and to infer read counts for individual genes. differentially expressed genes were identified using edger 3.4.2 […]


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EMSAR institution(s)
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Emerging Technology Center, DNA link, Seoul, Korea; Ewha Womans University, Seoul, Korea; Informatics Program, Boston Children’s Hospital and Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA

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