High quality Reference Transcriptome construction improves RNA-seq quantification in Oryza sativa ssp. indica

IndicaRTD.sh is a shell script used for the IndicaRTD construction.

jcc.R is the R script used for the validation of IndicaRTD annotation using Junction Coverage Compatibility (JCC) program.

EnsemblRTDgtf.sh, shell script used to convert the Oryza sativa ssp. indica Ensembl reference transcriptome fasta format file to GTF format.

multifilesgread.R, R script used for introns construction for the given reference transcriptome GTF file.