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Problems with gff3 file while running READemption

Hi!

I'm completely new to RNA Seq analysis and I can't cope with the problem. I'm trying to analyze dRNA Seq data from E. coli with READemption and segemehl. I managed to map the readings to the genome, but during gene expression quantification step and error occurs. It can't see the gff. Here's the error:

Error! Please make sure that you use the GFF3 formatted annotation files. GTF2/GTF is not valid and the usage of that format is not recommended.

There's also another 

ValueError: Invalid contig 'NC_000913.3'.

The gff (version 3) and genome files are from NCBI. How can I fix this?

Thanks for any suggestions!

rna-seq
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updated by Ram Ram • written by aq11 • aq11

Can you post some lines of your supppsed gff3? For example, first line (version), sequence-region pragma and a complete gene? Or the link to the annotation? like this one?

• 0 views • link
written by Carambakaracho Carambakaracho

It's the same file -gff and here's the genome sequence in fasta genome

• 0 views • link
written by aq11 • aq11

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