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chevron_left Known transcript quantification Alternative splicing events identification chevron_right
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SplAdder specifications

Information


Unique identifier OMICS_07841
Name SplAdder
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data All input formats follow the standardized formats for alignments and annotation such as BAM and GFF.
Input format BAM + GFF
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
h5py, pysam, scipy, matplotlib
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline André Kahles

Publication for SplAdder

SplAdder citations

 (5)
library_books

Position specific intron retention is mediated by the histone methyltransferase SDG725

2018
BMC Biol
PMCID: 5925840
PMID: 29706137
DOI: 10.1186/s12915-018-0513-8

[…] those found in 725ri-1 mutant plants [], indicating the distinct biological roles of these two h3k36-specific methyltransferases in rice., the splicing changes in rice were further analyzed by the spladder approach []. consistent with previous findings [], ir is the predominant form of as events identified by comparing to rice genome annotation (additional file : table s2). to perform […]

library_books

Innate Immune Response and Off Target Mis splicing Are Common Morpholino Induced Side Effects in Xenopus

2018
Dev Cell
PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] (n = 1,000). read coverage across exons, introns and splice junctions were normalized and averaged across biological triplicates (and developmental stages) to generate sashimi plots using spladder (). the consensus donor splice sequence (b) was derived from annotated canonical splice junctions detected by ≥10 split reads across all control samples (uninjected and wild-type) […]

library_books

Environment dependent regulation of spliceosome activity by the LSM2 8 complex in Arabidopsis

2017
Nucleic Acids Res
PMCID: 5499552
PMID: 28482101
DOI: 10.1093/nar/gkx375

[…] package () to generate a pileup file (coverage maps) for each sample. to detect alternative 5΄ splice site (a5΄ss), alternative 3΄ splice site (a3΄ss) and exon skipping (es) events, we employed the spladder software () using the highest confidence level. this toolbox takes the rna-seq alignments generated by tophat and the arabidopsis annotation data (tair10) as inputs to yield a splicing graph […]

library_books

A Comparison of RNA Seq Results from Paired Formalin Fixed Paraffin Embedded and Fresh Frozen Glioblastoma Tissue Samples

2017
PLoS One
PMCID: 5266269
PMID: 28122052
DOI: 10.1371/journal.pone.0170632

[…] transcript integrity number (tin) across all the transcripts and distribution of mismatches across reads were computed with rseqc [, ]. the percent spliced index (psi) values were calculated with spladder []. correlation plots and principal component analysis were done with custom r scripts., rsem read counts were used as input for deseq2 (version 1.10.1) [, ]. the cut-off for considering […]

library_books

Modulation of nonsense mediated decay by rapamycin

2016
Nucleic Acids Res
PMCID: 5389481
PMID: 27899591
DOI: 10.1093/nar/gkw1109

[…] v2.5.1b (). an expanded transcript annotation was generated using stringtie v1.2.3 () with gencode v19 as a reference annotation, and alternative splicing events were identified and quantified using spladder v1.0.0 (). paired differential splicing tests were performed using rmats-stat () with thresholds of δψ ≥ 0.1, δψ ≥ 0.05 and δψ > 0, and the resulting p-values were corrected for multiple […]


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SplAdder institution(s)
Memorial Sloan Kettering Cancer Center, New York, NY, USA; NICTA, Canberra Research Laboratory, Canberra, Australia
SplAdder funding source(s)
Funding was provided by the Max Planck Society, Memorial Sloan Kettering Cancer Center, by the German Research Foundation (RA1894/2-1) and the Lucille Castori Center for Microbes, Inflammation, and Cancer (No. 223316).

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