How to make an annotation file for reference genome?

Question

[Shahzad]

Dear All I need some guidance for RNA-seq analysis. I have RNA-seq data and want to analyze it. Reference genome is available as a multiple fasta files at NCBI. I have downloaded these files (approx. 300) and compiled to use it for reference genome. Now I need to know how to have an annotation file for mapping analysis so I could identify the differential expressed genes with my RNA-seq data. THANKS

Answer 1

[WouterDeCoster]

You need a .gtf or .gff file, which organism?

[Shahzad]

Sugarcane (Saccharum officinarum L.)

[wiatr.kalina]

Hey I have a similar question. I also have RNA-seq data and want to generate annotation file in .gtf, using UCSC (https://genome.ucsc.edu/cgi-bin/hgTables). However, I'm not sure what parameters should I use: -track - UCSC genes or Refseq genes? -table. I would be grateful for any tips from you.