Question: Disclaimer: Tried to post this on bioconductor support but it wont allow me. I tried adding an entire paragraph in "English language" but no - still wouldn't allow me.

Hi everyone,

I am using DEXSeq for exon quantification. I ran dexseq_prepare_annotation to convert gencode v24 GTF to GFF like this:

python2.7 ~/path/to/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py gencode.v23.annotation.gtf gencode.v23.annotation.gff

For IDO2 which has gene id ENSG00000188676, I got 18 exonic parts in the GFF:

grep 'ENSG00000188676' gencode.v23.annotation.gff

chr8 dexseq_prepare_annotation.py aggregate_gene 39934614 40016391 . + . gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39934614 39934954 . + . transcripts "ENST00000343295.8"; exonic_part_number "001"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39934955 39935218 . + . transcripts "ENST00000343295.8+ENST00000502986.2"; exonic_part_number "002"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39949149 39949165 . + . transcripts "ENST00000343295.8+ENST00000502986.2"; exonic_part_number "003"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39949166 39949264 . + . transcripts "ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "004"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39963608 39963703 . + . transcripts "ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "005"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39979067 39979186 . + . transcripts "ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "006"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39982652 39982770 . + . transcripts "ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "007"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39984951 39985507 . + . transcripts "ENST00000343295.8"; exonic_part_number "008"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39985508 39985522 . + . transcripts "ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "009"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39985523 39986460 . + . transcripts "ENST00000343295.8"; exonic_part_number "010"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39986900 39987085 . + . transcripts "ENST00000343295.8"; exonic_part_number "011"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39987743 39987870 . + . transcripts "ENST00000418094.1"; exonic_part_number "012"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39987871 39987970 . + . transcripts "ENST00000418094.1+ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "013"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 39989721 39989838 . + . transcripts "ENST00000418094.1+ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "014"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 40005327 40005378 . + . transcripts "ENST00000389060.8+ENST00000502986.2"; exonic_part_number "015"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 40013565 40013713 . + . transcripts "ENST00000418094.1+ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "016"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 40015247 40015605 . + . transcripts "ENST00000418094.1+ENST00000343295.8+ENST00000389060.8+ENST00000502986.2"; exonic_part_number "017"; gene_id "ENSG00000188676.13"
chr8 dexseq_prepare_annotation.py exonic_part 40015606 40016391 . + . transcripts "ENST00000418094.1+ENST00000343295.8+ENST00000502986.2"; exonic_part_number "018"; gene_id "ENSG00000188676.13"

However, when I go to [UCSC genome browser][1], it shows that IDO2 has 10 exons. Why does my GFF show 18 exonic parts or is there an issue with the conversion?

[1]: https://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc064mgi.1&hgg_prot=ENST00000389060.8&hgg_chrom=chr8&hgg_start=39949165&hgg_end=40015605&hgg_type=knownGene&db=hg38&hgsid=609990501_JhxAO5bBRafZjnld9AXbEMaABB6e

Answer: An "exonic part" is simply a part of an exon, so there will be at least as many of them as there are exons. Take the following example of a gene with two isoforms:

####--------####----
####------####----##

Here, `#` is an exon and `-` is intronic or intergenic region. I'll merge all of those exons together and then illustrate where the exonic parts are:

####------######--##
1111------223344--55 (1-5 indicate that the base above belongs to that `exonic part`)

You can see that the exons are divided into disjoint sections, where each "part" is shared completely by all of the transcripts that contain it (compare exon 2 in both of the isoforms, which are only partially shared between them).