SeqCluster protocols

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SeqCluster specifications

Information


Unique identifier OMICS_07768
Name SeqCluster
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data Count matrix
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.99.10
Stability Stable
Requirements
bcbio, pydebtools, pysam
Maintained Yes

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  • person_outline Eulalia Martí <>

Publication for SeqCluster

SeqCluster in pipeline

2017
PMCID: 5629335
PMID: 28860320
DOI: 10.1534/genetics.117.300221

[…] the sequence of each transcript was blasted against the a. gambiae pest repeatmasker library provided by vectorbase.org. for the small rna dataset. we generated a count matrix using seqbuster and seqcluster suites (). and used deseq2 () for differential expression analysis and log2 transformation of the count data. only putative small rna loci with a mean expression of >5 counts across […]


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SeqCluster in publications

 (3)
PMCID: 5837101
PMID: 29505615
DOI: 10.1371/journal.pone.0193527

[…] libraries were prepared with the nebnext® small rna library preparation kit and sequenced in an illumina hiseq2000 platform. mirnas, isomirs and clusters of small rnas were annotated using seqbuster/seqcluster framework in 5 plasma and 10 milk samples that passed the initial quality control. the rna yield was 81 ng/ml [standard deviation (sd): 41] and 3985 ng/ml (sd: 3767) for plasma and breast […]

PMCID: 5629335
PMID: 28860320
DOI: 10.1534/genetics.117.300221

[…] the sequence of each transcript was blasted against the a. gambiae pest repeatmasker library provided by vectorbase.org. for the small rna dataset. we generated a count matrix using seqbuster and seqcluster suites (). and used deseq2 () for differential expression analysis and log2 transformation of the count data. only putative small rna loci with a mean expression of >5 counts across […]

PMCID: 4306309
PMID: 25674563
DOI: 10.3389/fbioe.2015.00007

[…] in this case, it would seem reasonable to assume that the read should be mapped to the highly expressed rrna locus. some work has already been made toward overcoming these challenges. the tool seqcluster first fuses reads that overlap in sequence in a tiled way, and subsequently maps the fused sequences to the genome (pantano et al., ). these methods can resolve many, although not all, […]


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