'Problem with agat_sp_extract_sequences.pl
I did a genome prediction with Genemark and I am trying to extract sequences from GTF file obtained. I am using AGAT agat_sp_extract_sequences.pl command following the instruction provided by the help page but it is not working.
As output file I am obtaining this:
6637_t gene=6637_g seq_id="tig00055503 len=4381251 reads=16212 covStat=7603.97 gappedBases=no class=contig suggestRepeat=no suggestCircular=no" type=cds
6638_t gene=6638_g seq_id="tig00055503 len=4381251 reads=16212 covStat=7603.97 gappedBases=no class=contig suggestRepeat=no suggestCircular=no" type=cds
6639_t gene=6639_g seq_id="tig00055503 len=4381251 reads=16212 covStat=7603.97 gappedBases=no class=contig suggestRepeat=no suggestCircular=no" type=cds
6640_t gene=6640_g seq_id="tig00055503 len=4381251 reads=16212 covStat=7603.97 gappedBases=no class=contig suggestRepeat=no suggestCircular=no" type=cds
with no DNA sequences.
Did someone have an idea about why it happens?
Thanks for your help.
Sources
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Source: Stack Overflow
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