This has been asked before. That post contains a possible solution using BiomaRt using tximport to prepare salmon quantification files for DEG analysis. Also been asked on Bioc.

Hi ATpoint,thank you for the links, they gave me a direction how to proceed buy I still have issue... At the end seems that I can not download this file and I have to create it by myself.

The way I do is this

txdb <- makeTxDbFromGFF(file="~/RNAseq/annotation/genome/gencode.v19.annotation.gtf", format=("gtf"), , organism= "Homo sapiens")

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.


seqinfo(txdb)

Seqinfo object with 37 sequences (1 circular) from an unspecified genome; no seqlengths:
  seqnames   seqlengths isCircular genome
  chr1             <NA>       <NA>   <NA>
  chr2             <NA>       <NA>   <NA>
  chr3             <NA>       <NA>   <NA>
  chr4             <NA>       <NA>   <NA>
  chr5             <NA>       <NA>   <NA>
  ...               ...        ...    ...
  GL000212.1       <NA>       <NA>   <NA>
  GL000220.1       <NA>       <NA>   <NA>
  GL000228.1       <NA>       <NA>   <NA>
  GL000237.1       <NA>       <NA>   <NA>
  GL000241.1       <NA>       <NA>   <NA>

All the values are NA,\ I have tried also with different GFF files but the result doesn't change

this problem was shown also the in the link you gave to me but remain unsolved , Is there a specific package for you to create this file?(such as biomartr) , it has to be with two columns, one with gene ID and the other with trascripts

Thank you