IsoLasso protocols

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IsoLasso specifications

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Unique identifier OMICS_01320
Name IsoLasso
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.6.1
Stability Stable
Requirements
SAMtools, Libgsl-dev, Libcgal-dev
Source code URL http://alumni.cs.ucr.edu/~liw/isolasso-2.6.1.tar.gz
Maintained Yes

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Publication for IsoLasso

IsoLasso in pipeline

2013
PMCID: 3851429
PMID: 24268045
DOI: 10.1186/1471-2105-14-S14-S4

[…] for illustrative purposes, output from cufflinks [], is directly integrated into a tool pipeline. however, following our tool and file independent design approach, other reconstruction tools such as isolasso[] or trip[], and/or other quantification tools isoem[] or rsem[] may be utilized. finally, multiple myeloma and its associated cancer biology knowledge is utilized and structured […]


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IsoLasso in publications

 (5)
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w

[…] transcript quantification uses a statistical model for rna-seq reads to compute a point estimate of the isoform quantifications, extending an earlier unpaired model., cem, an extension of the method isolasso, constructs a connectivity graph to generate a set of candidate isoforms. cem and isolasso model the coverage of aligned reads at each location as a poisson distribution and use lasso […]

PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] the hypothesis is that the better the exon chains the better the traphlor should perform in comparison with stringtie., we attempted the downstream analysis also using cufflinks [], slide [], isolasso [] and flipflop []. but for the bigger read lengths with realistic error profiles, we were either unable to run the tools because of memory allocation errors (cufflinks, flipflop) […]

PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] rna-seq data, of which cufflinks () is the most widely used. other methods are stringtie (), scripture (), trinity (), oases (velvet) (), soap-denovo-trans (), ireckon (), class (), flipflop (), isolasso (), mitie (), trans-abyss (), augustus (), traph ()., algorithms are classified by whether they use an alignment to a reference genome sequence, or whether they assemble the reads into full […]

PMCID: 4331715
PMID: 25708199
DOI: 10.1186/1471-2164-16-S2-S15

[…] assembly usually begins by mapping rna-seq reads to the reference genome. after that, different algorithms can be used to infer transcripts from mapped reads, including cufflinks [,], isoinfer [], isolasso [], slide [], cliiq [], mitie [], etc. this ab initio approach is different from the de novo approach where reference genome is not used (such as abyss [], trinity [], etc.), and is able […]

PMCID: 4108029
PMID: 24739459
DOI: 10.1186/1471-2229-14-99

[…] the spliced reads that were not sufficiently supported were discarded as described in the methods section. secondly, we used three different software to reconstruct the transcripts: cufflinks [], isolasso [] and scripture []. since the 124 rnaseq libraries corresponded to 62 different replicated samples, we merged together the alignments from each replica, thus obtaining 62 datasets. […]


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IsoLasso institution(s)
Department of Computer Science and Engineering, University of California, Riverside, CA, USA; School of Life Science and Technology, Tongji University, Shanghai, China; School of Information Science and Technology, Tsinghua University, Beijing, China
IsoLasso funding source(s)
Funded by the NSF (grant IIS-0711129) and the NIH (grant AI078885).

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