Question: Cufflinks: reference annotation file for Nile Tilapia (Oreochromis_niloticus)
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gravatar for Fang,Xiefan
21 months ago by
Fang,Xiefan30
United States
Fang,Xiefan30 wrote:

I want to do differential gene expression analysis on some Nile Tilapia RNA-Seq data using the Cufflinks-Cuffdiff method. I aligned the sequence reads to the UCSC Nile Tilapia genome with >80% mapping efficiency. I downloaded the annotation GTF file from Ensembl and converted it using the "Make ensembl GTP compatible with Cufflinks" work flow. Then I ran cufflinks on the paired-end mapped data with either the original and converted GTF file. However, the counts were 0 for all gene and transcript expressionenter image description here. I noticed the the chromosome names of the Tilapia gtf file are strange. They are "GL831133.1" instead of 1,2,3. enter image description hereI also got zero readings using HTseq-count using either the original and converted GTF file. Does anyone know a good reference annotation file for Tilapia? Thanks!

ADD COMMENTlink written 21 months ago by Fang,Xiefan30
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gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

This workflow does not convert identifiers automatically in the correct format for all genomes. I can't see your pics, but the chromosome names do need to be a match between the reference genome and reference annotation. https://wiki.galaxyproject.org/Support#Reference_genomes

You could always download the reference genome from Ensembl and use that as a Custom Reference genome/build. Here is how: https://wiki.galaxyproject.org/Support#Custom_reference_genome

I am not aware of one that has all of the key attributes: tss_id, gene_id, gene_name, but others are welcome to comment.

Jen, Galaxy team

ADD COMMENTlink modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson24k

Thanks Jen. It turns out that the UCSC genome is OreNil2.0 and the ensembl annotation is OreNil1.0. I downloaded the ensembl tilapia genome (OreNil1.0) and did the tophat alignment again. This time, I could run cufflinks and HTseq with the ensembl annotation.

ADD REPLYlink written 21 months ago by Fang,Xiefan30
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