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Question: converty cuff id to gene id
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gravatar for mehdi.ramezani-moghadam
15 months ago by
mehdi.ramezani-moghadam • 0
mehdi.ramezani-moghadam • 0 wrote:

Hi, wondering if anyone could give me some clues how to convert cuff gene id to normal gene id so I know that gene im looking at? I have processed my samples through FASTQ groomer, Tophat, Cufflinks and then cuffdiff.

regards
rna-seq cufflinks name gene cuffdiff • 619 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by mehdi.ramezani-moghadam • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is an older reply but it covers the options available: https://biostar.usegalaxy.org/p/2053/

To link-in a gene identifier to a Cuffdiff result, do one of the following:

1 - Include a reference annotation dataset (GTF) during the workflow that contains the attribute gene_id (the gene name of interest) along with tss_id and p_id http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-input-files.

iGenomes is one source https://support.illumina.com/sequencing/sequencing_software/igenome.html

This reference annotation can be used with Tophat/HISAT2, Cufflinks, and Cuffmerge as well. See the workflow steps in the manual link above. Certain Galaxy RNA-seq tutorials can also be reviewed (some include these tools, others include alternative tools): https://galaxyproject.org/learn/

2 - Compare overlapping coordinates between your output and a tabular dataset (Interval or BED) containing genes/transcripts mapped to the same exact reference genome as used for the rest of the analysis. The tool mentioned in the first link above is one choice.

This question has been asked many times for various purposes, so please also see other related posts in the right side bar for more options and special cases.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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