RACKJ protocols

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chevron_left Alternative splicing events identification Known transcript quantification File comparison Differential usage Read alignment visualization chevron_right
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RACKJ specifications

Information


Unique identifier OMICS_07373
Name RACKJ
Alternative name Read Analysis & Comparison Kit in Java
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.95
Stability Stable
Maintained Yes

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  • ShuffleFastq

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Additional information


http://rackj.sourceforge.net/Manual/index.html https://sourceforge.net/projects/rackj/?source=navbar

Publication for Read Analysis & Comparison Kit in Java

RACKJ in pipelines

 (5)
2018
PMCID: 5849712
PMID: 29535339
DOI: 10.1038/s41598-018-22406-6

[…] with more than one gene models in the genome annotation, the longest one was selected for the calculation., splicing patterns were explored using the read analysis & comparison kit in java (rackj) software toolbox (http://rackj.sourceforge.net/), which separately calculates the number of reads matched to exons, introns and splice junctions,,. to diminish the number of potential false […]

2018
PMCID: 5873924
PMID: 29487188
DOI: 10.1534/g3.118.200022

[…] 4bp exact matches in both ends were accepted. rest reads were mapped to the tair10 genome using blat (), where alignments with blocks shorter than 8bps were removed. read counts were computed using rackj (http://rackj.sourceforge.net/) and normalized into log-count-per-million (logcpm) using the tmm method () and the voom method (). logcpm values were then transformed into rpkm values. […]

2016
PMCID: 4981272
PMID: 27317682
DOI: 10.1534/genetics.116.190751

[…] default setting. only best alignments with an identity of no less than 90% were accepted for computation and >95% of reads were accepted for every replicate (see table s2 for mapping statistics). rackj (http://rackj.sourceforge.net) was then used to compute the read counts of all genes and average the depths of all exons and all introns., the read counts of all samples were normalized using […]

2016
PMCID: 5090222
PMID: 27804982
DOI: 10.1038/srep35846

[…] gene expression levels, 75-mers sequences were aligned to the genomic sequence annotated in tair10 using the blat program and rpkm (reads per kbp per million reads) values were computed using the rackj (read analysis & comparison kit in java, http://rackj.sourceforge.net/) software., gene clustering was performed using the maccu software package (http://maccu.sourceforge.net/) to build […]

2015
PMCID: 4458573
PMID: 26106402
DOI: 10.3389/fpls.2015.00421

[…] by rna-seq from two biological repeats. the rna-seq data was subsequently analyzed using blat program (kent, ) and the differentially expressed genes were further mined by custom-made software rackj (lan et al., ). in the present study, the rna-seq data were re-analyzed by aligning the paired-end reads to arabidopsis genome released in tair10 via tophat program (trapnell et al., ). […]


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RACKJ in publications

 (9)
PMCID: 5849712
PMID: 29535339
DOI: 10.1038/s41598-018-22406-6

[…] intron retention (ir), alternative donor (altd), alternative acceptor (alta), and alternative position (altp, in which both donor and acceptor sites are different). based on the mapping results, rackj was used to compute the following read counts, and the results were separated into several tables: (1) for each exon, (2) for each intron, (3) for each exon-pair that was mapped by spliced […]

PMCID: 5507634
PMID: 28706989
DOI: 10.1126/sciadv.1602878

[…] position were then filtered out. prinseq lite v.0.20.4 () was then used to find read pairs that passed the filtering conditions. these read pairs were then interleaved into a single file using the shufflefastq script in rackj v.0.95 (http://rackj.sourceforge.net/scripts/index.html#shufflefastq)., dna libraries were also constructed for the malayan tapir (tapirus indicus), black rhinoceros (d. […]

PMCID: 4848314
PMID: 27200029
DOI: 10.3389/fpls.2016.00555

[…] obtained in each sample. all clean reads were mapped to the tair10 genome. rpkm (reads per kilobase of exon model per million mapped reads; ) values were computed based on these mapped reads using rackj, and student t-tests were carried out based on rpkm values. genes were consider as significantly differentially expressed with a p-value < 0.05 and relative change threshold of twofold. go […]

PMCID: 4753498
PMID: 26875681
DOI: 10.1038/srep21589

[…] the filtered reads were sorted to retain only paired-end reads (prinseq). paired-end reads were interleaved into a single file before contig assembly, for a total of 12 quality-filtered fastq files (rackj). the trinity assembler was used to construct contigs from the quality-filtered fastq files. each library was assembled separately, using default parameters and paired-end reads., contigs […]

PMCID: 4458573
PMID: 26106402
DOI: 10.3389/fpls.2015.00421

[…] matched to arabidopsis genome in each biological repeat using blat program (kent, ) and the differentially expressed genes were then identified in each replication using custom-made software rackj (lan et al., ), which results in 1617 differentially expressed genes between root hairs (herein referred as rh) and non-root hair tissues (all root tissues except root hairs; herein referred […]


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RACKJ institution(s)
Institute of Plant and Microbial Biology, Taipei, Taiwan

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