Using ensembl genomes and gtf conversion
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5.7 years ago
as9309 ▴ 40

Hi,

I'm trying to align my RNA-seq data to an E coli reference genome that I downloaded from Ensembl bacteria but I'm getting stuck because I need the genome in gtf format. I can only download it in gff3 and cannot convert gff3 to gtf because gffread does not work ("Uncaught exception in exposed API method:").

Does anyone know either how I can align my data to the most current E coli reference genome or convert my gff3 to gtf without the requirement of gffread?

I have previously tried to convert an ensembl gtf to the correct format ("https://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq") but it gives me a tabular output - can I change this?

Thanks!

RNA-Seq genome conversion gffread • 2.2k views
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GFF3 is supposed to be a backwards compatible specification of the GFF tabular format and GTF, as far as I understand it, is similar to GFF2. So what is your requirement for converting GFF3 to GTF and why is a tabular output not the correct one?

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When I use cufflinks with the gff3 file, it provides the correct gene annotation but with incorrect gene names. e.g. instead of the RpoS gene, it gives me "transcript:AAC75783". Also, the cufflinks programme will not recognise my .tab file. Do you know how I can rearrange the gff3 file to identify the gene with their names instead of transcript number?

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Could it be because your file doesn't have a .gtf or .gff extension ? If you're using files from Ensembl, those should be in GTF format with the proper .gtf extension. If using GFF3, do you have a gene_name attribute ?

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Yes, worked with the gff3 file! Thanks for your help.

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5.7 years ago

It might be worth specifying what pipeline you're trying to use, Tuxedo maybe? Considering you're using gffread. Just to make sure that you're using the GTF from here right - that should be in GTF format already...?

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Thanks for your reply - yes I took the MG1655 genome from Ensembl bacteria but when I upload to galaxy, it recognises it as a gff file.

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If you're performing this on galaxy then I'd suggest you check out the Galaxy Wiki which includes mailing lists for support.

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