Question: Finding gene names from TopHat results.
gravatar for hamza_karakurt
5 weeks ago by
hamza_karakurt10 wrote:

Hello, I am trying a build a workflow for RNA-Seq analysis and I want to verify my methods via comparing a data set. The data sets I am trying to use are GSE56016 and GSE36537 from NCBI GEO. They have only one RNA-Seq result. I downloaded fasta from EBI SRA did analysis. I used TopHat and want to compare the accepted hits results. The results from NCBI GEO includes gene names in accepted hits files but my result does not have any gene names. I converted them to BED files via BAMtoBED tool but I still do not have any gene names.

How can I extract the gene names from accepted hits files?

Thank you.

tophat bed genenames bam • 57 views
ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson23k • written 5 weeks ago by hamza_karakurt10
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:


The BAM results have gene names in them? Was the data mapped against an exome/transcriptome?

You could do the same if that fasta file is available. Use it as a "custom genome".

If instead you mapped against a reference genome and can find an annotation dataset that is based on that same reference genome, you can visualize the two track together and do downstream RNA-seq analysis.


Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson23k
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