SplitSeek protocols

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chevron_left Novel transcript quantification Alternative splicing events identification chevron_right
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SplitSeek specifications

Information


Unique identifier OMICS_01253
Name SplitSeek
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format BED, BEDPE
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Adam Ameur <>

Publication for SplitSeek

SplitSeek in pipeline

2010
PMCID: 2926789
PMID: 20653958
DOI: 10.1186/gb-2010-11-7-r78

[…] on the ontology of biological processes and considered a corrected (benjamini) p-value < 0.01 to be significant., to detect splice junctions, we analyzed the reads using the version 1.3.2 of the splitseek algorithm [], available from the solid software development community []. since the splitseek algorithm is not applicable for the shorter read lengths, we used only the 50-bp reads […]


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SplitSeek in publications

 (7)
PMCID: 4648566
PMID: 26609224
DOI: 10.4137/BBI.S28991

[…] of short reads or de novo assembly and characterization of transcript models. examples of these methods are miso for identification and regulation of isoforms from clip-seq data and splicemap, splitseek, splicer, and splicingcompass for detection of splice junctions and exon usage from pair-end rna-seq. glimmps provides a useful tool for elucidating the genetic variation of alternative […]

PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] of databases related to rna-seq data for ncbi for inclusion into an as database., the common as site prediction software includes erange, qpalma [], tophat, mapsplice [], splicemap, soapsplice, splitseek [], and hmmsplicer. current studies using rna-seq to identify as sites focus on locating splice sites, discovering new splice sites located as distantly as possible, and conducting […]

PMCID: 3592422
PMID: 22941640
DOI: 10.1093/nar/gks816

[…] as our result shows that a higher fraction of the exomernaseq reads map to exons, we next sought to identify splice junctions and novel exons in the capture data. we used tophat () and splitseek () on our sequencing results to identify splice junctions in each sample and found similar results with both algorithms (data not shown). on average, 100 000 junctions were identified […]

PMCID: 3595467
PMID: 22531089
DOI: 10.1038/ijo.2012.57

[…] error of the solid sequencing was 5% and 8% (relative error 0.10 and 0.17) in the obese and control pool, respectively., small insertions and deletions (indels) were called with two methods: splitseek, which realigns unmapped reads from corona lite; and gapped alignments using bwa and samtools. indels were only considered valid if they were called by both approaches and frequencies, […]

PMCID: 3226252
PMID: 21988959
DOI: 10.1186/1471-2105-12-S5-S2

[…] such as g-mo.r-se [] and tophat [] perform a global search of splice junctions. however, g-mo.r-se is limited by its inability to handle pe reads, whereas tophat depends on canonical splice codes., splitseek [], supersplat [], and splicemap [] were recently proposed to perform truly global and unbiased spliced-read mapping. these methods, however, rely on an arbitrary read-count method […]


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SplitSeek institution(s)
Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
SplitSeek funding source(s)
Supported by the Swedish Natural Sciences Research Council.

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