# Create restructured.gff for the ggtranscript
## gff files are stored under InputFiles/gff_files for each sample with the file name: scisoseq_transcripts.sorted.filtered_lite.gff  

less scisoseq_transcripts.sorted.filtered_lite.gff  | cut -fess | sed 's/;/ /g' | less | awk '{print $2}' > genesNames_gff.gff
less scisoseq_transcripts.sorted.filtered_lite.gff  | cut -fess | sed 's/;/ /g' | less | awk '{print $4}' > transcriptNames_gff.gff
less scisoseq_transcripts.sorted.filtered_lite.gff | cut -f1,4,5,7 > seqname_start_end.gff
less scisoseq_transcripts.sorted.filtered_lite.gff | cut -f3 | less > exons.gff
paste seqname_start_end.gff exons.gff genesNames_gff.gff transcriptNames_gff.gff | sed 's/"//g' | sed 's/ /\\t/g' > restructured.gff
