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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