SeqEM protocols

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SeqEM statistics

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SeqEM specifications

Information


Unique identifier OMICS_00074
Name SeqEM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Eden Martin <>
  • person_outline SeqEM Team <>

Publication for SeqEM

SeqEM in pipelines

 (2)
2015
PMCID: 4982090
PMID: 26358618
DOI: 10.1111/1755-0998.12465

[…] profiles (mortazavi et al. ). some annotation tools have been developed to help deal with these problematic sequences, such as erange (mortazavi et al. ), bm‐map (ji et al. ), rsem (li et al. ) and seqem (paşaniuc et al. ). however, our results demonstrate that the inclusion of multimatch reads, or indeed contigs that map to multiple genes, in any transcriptome study of a species lacking […]

2013
PMCID: 3823931
PMID: 24244370
DOI: 10.1371/journal.pone.0078823

[…] of mapped reads, resulting in a per gene expression metric: reads per kilobase per million mapped (rpkm). reads that had between two and five valid alignments were assigned a single location using seqem ., a subset of 5% (108,362) of the germline polymorphisms in ludlu-1 were selected, at random, for comparison with the somatic variants. all single nucleotide substitutions were annotated using […]


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SeqEM in publications

 (3)
PMCID: 5522067
PMID: 28178688
DOI: 10.18632/oncotarget.15039

[…] reads were pre-processed to check read metrics, filter and then trimreads. reads were aligned to the human reference genome version 19 using tophat. multireads were assigned using the programme seqem []. data were expressed as counts per million: 106. z.cx/ln, where z is the normalization factor (mean length of expressed transcripts), cx the number of reads mapping to transcript x, l […]

PMCID: 3166303
PMID: 21912681
DOI: 10.1371/journal.pone.0024248

[…] were detected in any of the samples analyzed., to determine differences in mirna expression patterns in glioblastomas versus non-tumor brain tissue, we used the mirnakey pipeline, implementing the seqem option to account for reads mapping to multiple mirnas . 449 mature mirnas and mirnas* were identified using a filter of rpkm score >1 to normalize read counts between different libraries […]

PMCID: 3216542
PMID: 22355574
DOI: 10.1038/srep00055

[…] variation from the sequencing error or mapping error., currently, there are several methods available for calling snps from ngs data, including pyrobayes, polybayes, maq, soapsnp, varscan, snvmix, seqem and atlas-snp2. pyrobayes and polybayes recalibrate base calling from raw data, and then implement a bayesian approach that incorporates prior information with population mutation rates […]


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SeqEM institution(s)
John P Hussman Institute for Human Genomics and the Dr John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
SeqEM funding source(s)
Supported by National Human Genome Research Institute (RC2HG005605), National Institute for Neurology and Stroke (U54NS065712 and R01NS026630).

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