SOAPsplice statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

SOAPsplice specifications

Information


Unique identifier OMICS_01251
Name SOAPsplice
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.10
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


download.png
conda.png

Versioning


No version available

Maintainers


  • person_outline Siu-Ming Yiu
  • person_outline Zhiyu Peng

Additional information


https://bioconda.github.io/recipes/soapsplice/README.html

Publication for SOAPsplice

SOAPsplice citations

 (11)
library_books

Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis

2016
PLoS One
PMCID: 4961362
PMID: 27459697
DOI: 10.1371/journal.pone.0159719

[…] We used SOAPsplice software with a default setting and RNA-Seq data to detect splice junctions and identify the potential AS patterns of genes (Fig B in ). SOAPsplice uses a novel approach comprising the foll […]

library_books

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA sequencing

2016
Sci Rep
PMCID: 4827084
PMID: 27063004
DOI: 10.1038/srep24141

[…] For transcriptomic analyses, quality-score filtered sequences were aligned to the human genome assembly of Ensembl (GRCh37/ hg19, Feb 2009, Version 72) using the SoapSplice alignment software. The number of uniquely mapping reads was estimated for each sample by using HTSeq-Count. Gene expression read counts were used to identify differential expressed genes ( […]

library_books

Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

2016
BMC Plant Biol
PMCID: 4750186
PMID: 26865323
DOI: 10.1186/s12870-016-0726-3

[…] of mappable reads that fell onto the genes; N is the total number of maptable reads in the experiment; L is the sum of the genes in base pairs).Alternative splicing transcripts were analyzed based on SOAPsplice software []. For novel transcripts which were not identified in the TAIR10.0 database, the assembled transcripts must meet the following three criteria: (i) the length of the transcript mus […]

call_split

MicroRNA 222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells

2016
PMCID: 4849150
PMID: 26844700
DOI: 10.1038/cddis.2016.10
call_split See protocol

[…] 81, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75981). Analysis of count data was performed using htseq-count (v0.5.3p9) and DESeq2 after reads were aligned to the mouse genome (mm10) using SOAPSplice. In brief, DESeq2 uses generalized linear models based in the negative binomial distribution. We built linear models using two different experiments and two conditions (miR-222 overexpressi […]

library_books

Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico

2015
Biomed Res Int
PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] ese factors on AS research was analyzed. Using RNA-seq data produced by the Illumina/Solexa sequencing platform as an example, we compared three common splice site prediction programs (HMMSplicer [], SOAPsplice, and TopHat []) under conditions of different depths and sequence read lengths. The performance of each type of software was evaluated under different conditions by comparing the number of […]

library_books

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

2015
Retrovirology
PMCID: 4434878
PMID: 25980612
DOI: 10.1186/s12977-015-0165-5

[…] 0 mio read pairs were obtained for the samples. Sequencing reads were quality filtered before alignment using Cutadapt [] and PrInseq []. Cleaned sequencing reads were aligned to a build genome using SOAPsplice. Gene expression was assessed by determining the number of mapped reads per gene using HTSeq-count tool, followed by DESeq R package normalization. An additional normalization step taking i […]

Citations

Looking to check out a full list of citations?

SOAPsplice institution(s)
Bioinformatics Center, Beijing Genomics Institute at Shenzhen, Shenzhen, China; Department of Computer Science, The University of Hong Kong, Hong Kong, China

SOAPsplice reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SOAPsplice