Where to find a valid GTF file for stringtie asssembly?

Question

[lakhujanivijay]

Hi all

I am trying to locate a valid GTF file for transcriptome assembly of Cenchrus americanus (Pearl Millet) for the genome information avaialble at this NCBI link here.

Assembly with Stringtie the GFF file downloaded from here does not work and throws following error.

$ stringtie -p 55 -c 10 -G cenchrus_americanus.gff -l A -o A.gtf -C A.ref.transcript.covered.txt A.sorted.bam

Error: could not any valid reference transcripts in cenchrus_americanus.gff (invalid GTF/GFF file?)

It is obvious as the GFF file does not contain information for transcripts, just a single type of field in the 3rd column

$ awk -F "\t" '{print $3}' cenchrus_americanus.gff | sort | uniq

region

There is only this paper which I could find (referenced to the genome provided by NCBI)

There is one other link which I found here and which have a couple of files, however, not sure what all do they mean. Can anybody help me with finding the proper GTF file ? Lastly, I also looked at Ensembl plants database with no luck!

Thanks

Vijay

[c_u]

hey, did you find the GTF file you were looking for? I am also looking for it

Answer 1

[Damian Kao]

The .gff file you downloaded doesn't describe gene annotations. It just describes the genome scaffolds/contigs. There doesn't appear to be any gene annotations in the NCBI ftp you posted.

You do not need to provide StringTie with a set of reference annotations. You can perform an assembly just with your transcriptome reads.

[lakhujanivijay]

The .gff file you downloaded doesn't describe gene annotations.

Yes , exactly!

You do not need to provide StringTie with a set of reference annotations.

I am attempting reference-based transcriptome assembly. Any clues for me?