RACKJ statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RACKJ

Tool usage distribution map

This map represents all the scientific publications referring to RACKJ per scientific context
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RACKJ specifications


Unique identifier OMICS_07373
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


  • ShuffleFastq




No version available

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 citations


A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana

PMCID: 5873924
PMID: 29487188
DOI: 10.1534/g3.118.200022
call_split See protocol

[…] t 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. Different […]


Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades

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

[…] se 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. bic […]


Systems wide analysis of manganese deficiency induced changes in gene activity of Arabidopsis roots

Sci Rep
PMCID: 5090222
PMID: 27804982
DOI: 10.1038/srep35846
call_split See protocol

[…] ify 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. […]


Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana

PMCID: 4981272
PMID: 27317682
DOI: 10.1534/genetics.116.190751
call_split See protocol

[…] the 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 the […]


Genome Wide Analysis of Gene Regulatory Networks of the FVE HDA6 FLD Complex in Arabidopsis

Front Plant Sci
PMCID: 4848314
PMID: 27200029
DOI: 10.3389/fpls.2016.00555
call_split See protocol

[…] re 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 terms […]


Re analysis of RNA seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs

Front Plant Sci
PMCID: 4458573
PMID: 26106402
DOI: 10.3389/fpls.2015.00421

[…] parately 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 as […]

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

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