According to article(Castandet B, Hotto A M, Strickler S R, et al. ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress), I entered the following command：
./chloroseq.pl -a 2 -b ./../../tophat_out664/accepted_hits.bam -e ./../TAIR10_ChrC_files/TAIR10_ChrC_exon.gff3 -i ./../TAIR10_ChrC_files/TAIR10_ChrC_introns.gff3 -g 154478 -n NC_000932.1 Arabidopsis thaliana chloroplast, complete genome -s ./../TAIR10_ChrC_files/TAIR10_ChrC_splice_sites_sort.gff3
But then the computer shows：
Starting prep_bam.sh. Starting splicing analysis (Analysis 2). Need to supply splice file
I think I may not have figured out what splice file means. And is the series of gff3 files I am using correct?
According to article(Castandet B, Hotto A M, Strickler S R, et al. ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress), I entered the following command：
./chloroseq.pl -a 2 -b ./../../tophat_out664/accepted_hits.bam -e ./../TAIR10_ChrC_files/TAIR10_ChrC_exon.gff3 -i ./../TAIR10_ChrC_files/TAIR10_ChrC_introns.gff3 -g 154478 -n NC_000932.1 Arabidopsis thaliana chloroplast, complete genome -s ./../TAIR10_ChrC_files/TAIR10_ChrC_splice_sites_sort.gff3But then the computer shows：Starting prep_bam.sh. Starting splicing analysis (Analysis 2). Need to supply splice fileI think I may not have figured out what splice file means. And is the series of gff3 files I am using correct?