Tag: Junction

RJPrimers 1.0 – Transposable Element Junction based PCR Primer Design

RJPrimers 1.0

:: DESCRIPTION

RJPrimers is a high-throughput software tool to identify unique repeat junction and design TE-based primers for high-throughput marker development. This tool first identifies potentially unique repeat junctions using BLAST against fully annotated repeat databases and a repeat junction finding algorithm, and then designs TE based primers using Primer3 and BatchPrimer3.

::DEVELOPER

GrainGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak and Yong Q. Gu.
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
Nucl. Acids Res. (2010) 38 (suppl 2): W313-W320. doi:10.1093/nar/gkq425

Portcullis 1.2.2 – Splice Junction Analysis and Filtering from BAM files

Portcullis 1.2.2

:: DESCRIPTION

Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Portcullis

:: MORE INFORMATION

Citation

Gigascience. 2018 Dec 1;7(12). doi: 10.1093/gigascience/giy131.
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.
Mapleson D, Venturini L, Kaithakottil G, Swarbreck D.

SpliceJumper – Splicing Junction Calling from RNA-Seq data

SpliceJumper

:: DESCRIPTION

SpliceJumper is a classification based approach for calling splicing junctions from RNA-seq data

::DEVELOPER

Simon C Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SpliceJumper

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 17:S10. doi: 10.1186/1471-2105-16-S17-S10. Epub 2015 Dec 7.
SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.
Chu C, Li X, Wu Y.