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Question: Cufflinks C. elegans no gene names?
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gravatar for razbarz
7 months ago by
razbarz • 0
razbarz • 0 wrote:

Hello, I have a question regarding cufflinks. I used HISTAT2 for alignment using this file - c_elegans.PRJNA275000.WS263.genomic.fa Then I ran cufflinks with this annotation file c_elegans.PRJNA275000.WS263.annotations.gff3.gz

I get FPKM values but no gene names. What happened? I thought that since I got the alignment reference and the annotation from the same source they should work?

Please help.

Thanks
rna-seq cufflinks • 205 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by razbarz • 0
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The reference annotation must include the tss_id, gene_id, and gene_name attributes to have those values incorporated by this tool. Your annotation file is probably missing: gene_name.

iGenomes is a common source for annotation data to use with this tool suite. https://support.illumina.com/sequencing/sequencing_software/igenome.html

Make sure to pick the version that matches the target reference genome source/build. UCSC's ce10 is indexed for HISAT2 at Galaxy Main https://usegalaxy.org and has a matching annotation file at the iGenomes data site. Download the tar archive locally, uncompress it, then upload just the genes.gft annotation file to Galaxy.

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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