Question: cDNA in TopHat
gravatar for cased
14 months ago by
cased0 wrote:


I am new here so first, nice to meet to all of you.

I am a PhD Student and I have a question about tophat and the reference genome.

On one hand, I have been using the reference genome with the gtf file for the alignment with tophat. On the other hand, I have been using the coding reference genome (cDNA) for the alignment with salmon.

My question is the following:

Can I use the cDNA with tophat and the gft? Because I need the BAM files and the count with tophat for a set of data but, I am interested also in the integration of these data with the data belonging to salmon. I supposed that if the data hasn't been extracted with the same reference genome, I can't integrated them.

rna-seq tophat • 465 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by cased0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


NGS reads can be mapped against a transcriptome database as a Custom reference genome. A spliced alignment tool wouldn't be needed, instead, use a tool like Bowtie2 or BWA/BWA-MEM. Your GTF describing annotation on the primary reference genome wouldn't be used (genome mismatch).

Thanks! Jen, Galaxy team

Galaxy tutorials for reference:

ADD COMMENTlink modified 13 months ago • written 14 months ago by Jennifer Hillman Jackson25k

Thank you very much Jennifer. The link to the Custom Reference genome doesn't work, I can't go to this page. One more question, if I want to work with the transcriptome, I can use tophat2 and then, cufflinks right?

Thank you in advance.

Best regards.

ADD REPLYlink written 14 months ago by cased0

Hi - sorry, fixed the link. Yes, you could use these tools, although HISAT(2) is now preferred over Tophat (the Tophat tool is considered deprecated and replaced by HISAT). From there are several tool options for transcript assembly or count based differential expression. See the RNA-seq tutorials in the link above for examples.

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k
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