Hello,
Thank you so much for the development of RSEM.
I am trying to run the RSEM in a non model species, however after many trials I having issues with the gtf. If it is possible I will like to ask which kind of information should be contained in the gtf. My actual gtf have an structure of 9 genes where one have two types of transcript (in total 10 entries).
The entries are like the following (one gene example):
Hello, Thank you so much for the development of RSEM. I am trying to run the RSEM in a non model species, however after many trials I having issues with the gtf. If it is possible I will like to ask which kind of information should be contained in the gtf. My actual gtf have an structure of 9 genes where one have two types of transcript (in total 10 entries).
The entries are like the following (one gene example):
gff-version 3
Chr_scaffold_ancX GINGER CDS 62941173 62949964 . + . gene_id "Cdx4.cds1";transcript_id "Cdx4.mrna1"; Chr_scaffold_ancX GINGER mRNA 62941173 62949964 . + . gene_id "Cdx4.mrna1";transcript_id "Cdx4.mrna1"; Chr_scaffold_ancX GINGER gene 62941173 62949964 . + . gene_id "Cdx4.mrna1";transcript_id "Cdx4.mrna1"; Chr_scaffold_ancX GINGER exon 62941172 62941837 . + . gene_id "Cdx4-exon1";transcript_id "Cdx4.mrna1"; Chr_scaffold_ancX GINGER exon 62947725 62947870 . + . gene_id "Cdx4-exon2";transcript_id "Cdx4.mrna1"; Chr_scaffold_ancX GINGER exon 62949186 62949964 . + . gene_id "Cdx4-exon3";transcript_id "Cdx4.mrna1";
Could you gimme some hints about the structure need it to run the program?