Table 1 List of software packages and scripts used in CANEapp
From: CANEapp: a user-friendly application for automated next generation transcriptomic data analysis
Software name | Function | CANE module |
|---|---|---|
SRA tools | FASTQ extraction from the SRA file format | Alignment and reconstruction |
TopHat | Read alignment | Alignment and reconstruction |
STAR | Read alignment | Alignment and reconstruction |
Cufflinks | Ab initio transcript reconstruction | Alignment and reconstruction |
Cuffcompare | Merging transcripts | Transcript filtering and classification |
Samtools | Nucleotide sequence extraction | Transcript filtering and classification |
CNCI | Coding potential prediction | Transcript filtering and classification |
Cuffdiff | Differential expression testing | Gene expression and results formatting |
HTSeq | Counting reads in loci | Gene expression and results formatting |
edgeR (R package) | Differential expression testing | Gene expression and results formatting |
DESeq2 (R package) | Differential expression testing | Gene expression and results formatting |
Primer 3 | Primer sequence retrieval | Primer design |