Question: Using a reference transcriptome as a custom genome with tools
gravatar for biopili9
19 months ago by
biopili910 wrote:


I want to know if I can build a transcriptome using the sequences of other transcriptome that was published previously in genbank?

Can use how reference a transcriptome previously published?

Can I compare in the same work sequences made with illumina hiseq-2000 and hiseq2500?

ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by biopili910
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:


For the first part, almost any fasta file can be uploaded and used as a Custom Reference Genome with tools. A Custom Genome can also be of transcript content, the label is general and can apply to both.

Be aware that if the transcript dataset is highly fragmented (sometimes the result from assembly), you might run into memory issues when running jobs at Sometimes filtering by length can help (to remove small sequences that didn't fit into the larger assembly, some of which could be contamination of some sort). Still, give it a try first. Jobs that do require more memory (the job will fail with a specific error) could be run on a local/cloud Galaxy with boosted resources allocated.

Help links:

For the second part, do you mean that you wish to map the NGS reads against the transcriptome? That is certainly possible and a how-to, including a few video examples, are included in the first help link above. If you want to do something else with these data, please reply with more details about what your analysis goals are.

RNA-seq tutorials can be found here. Using your custom genome (aka transcriptome) instead of a pre-indexed genome on the server is definitely possible.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson25k
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