Corset protocols

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Corset specifications

Information


Unique identifier OMICS_12944
Name Corset
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.07
Stability Stable
Requirements
SAMtools
Maintained Yes

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Documentation


Maintainer


  • person_outline Alicia Oshlack <>

Additional information


https://github.com/Oshlack/Corset/wiki

Publication for Corset

Corset in pipelines

 (10)
2018
PMCID: 5919011
PMID: 29694395
DOI: 10.1371/journal.pone.0195913

[…] (version 2.0.6) with default parameters [, ]. the paired-end reads from each library were mapped to de novo assemblies using bowtie (version 1.1.1) []. the transcript abundance was estimated using corset (version 1.03) []. the count data generated from corset were processed using the edger package []. transcripts with less than one count per million reads (cpm) for at least three libraries […]

2017
PMCID: 5515871
PMID: 28769963
DOI: 10.3389/fpls.2017.01260

[…] (table ). given the lack of c. trapeziformis genome, reconstruction of the floral transcriptome for the 464.6 m high-quality pe reads used a three-step strategy involving trinity (), bowtie (), and corset (), producing 686,243 contigs in the preliminary assembly. the final assembly consists of 221,668 contigs retained by corset (supplementary data , ) – effectively removing many short contigs […]

2017
PMCID: 5595854
PMID: 28900192
DOI: 10.1038/s41598-017-11588-0

[…] parameters, . the filtered reads from each library were mapped to de novo assemblies using bowtie version v1.1.1 by allowing two mismatches (-v 2 -m 10). the transcript abundance was estimated using corset (version 1.03). the count data generated from corset were processed using the edger package. transcripts with less than one count per million reads (cpm) for at least three libraries […]

2017
PMCID: 5695279
PMID: 29125846
DOI: 10.1371/journal.pone.0187738

[…] a total of 219,831 transcripts with average length of 771 bp and n50 of 1302 bp (). the length distribution of transcripts is showing in . the de novo assembled transcriptomes were clustered by ‘corset’, which is a method and software for obtaining gene-level counts from any de novo transcriptome assembly []. after clustering by corset, a total of 139,863 clusters were obtained, […]

2017
PMCID: 5717322
PMID: 29242829
DOI: 10.1128/mSphere.00094-17

[…] were mapped against the assembled reads using bowtie 2 () (with the following parameters: --end-to-end; --no-mixed; --no-discordant; --score-min l,-0.1,-0.1) and were clustered into genes using corset software (minimum read count = 5) (). a few bacterial sequences were detected through blast searches against the ncbi-nr database and were removed from subsequent analysis. statistically […]


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Corset in publications

 (22)
PMCID: 5919011
PMID: 29694395
DOI: 10.1371/journal.pone.0195913

[…] (version 2.0.6) with default parameters [, ]. the paired-end reads from each library were mapped to de novo assemblies using bowtie (version 1.1.1) []. the transcript abundance was estimated using corset (version 1.03) []. the count data generated from corset were processed using the edger package []. transcripts with less than one count per million reads (cpm) for at least three libraries […]

PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] (contig12688) was also up-regulated in severe malaria (p = 0.0537). dc5 was up-regulated in severe malaria in africa [] and expressed in a cerebral malaria case in papua new guinea []., corset [] groups transcripts together based on the number of reads that multi-map between them whilst ensuring transcripts are not combined if they have significantly different expression profiles. […]

PMCID: 5775280
PMID: 29379412
DOI: 10.3389/fnins.2017.00752

[…] for neural and y-organ tissues, and a third comprising yo and epidermis tissues, were assembled separately. differential gene expression analysis between yo and epidermis tissues was done using corset (davidson and oshlack, ) and edger (robinson et al., ) to identify gpcrs upregulated in the yo relative to the epidermis. transcriptomes were mined for contigs putatively encoding neuropeptide […]

PMCID: 5873896
PMID: 29580381
DOI: 10.7554/eLife.33399.035

[…] was used to map individual sample to the respective transcriptome assemblies using default parameters. further, to improve the read count estimation and reduce the redundancy in trinity transcripts, corset () was implemented to estimate raw read counts using the bowtie2 mapped alignment data. the obtained raw read counts were normalized and differentially expressed genes (padj <0.01) […]

PMCID: 5748711
PMID: 29257091
DOI: 10.3390/genes8120393

[…] program trinity using clean reads []. the high-quality transcripts were obtained after filtering and assembling. these transcripts were utilized for the further process of sequence clustering with corset to create unigenes []. next, a follow-up analysis was carried out with these unigenes, which were assembled from scratch. the published transcriptomes of other pinus species from the ncbi […]


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Corset institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC, Australia
Corset funding source(s)
Supported by an NHMRC Career Development Fellowship APP1051481.

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