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Question: Using a reference transcriptome as a custom genome with tools
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gravatar for biopili9
19 months ago by
biopili9 • 10
biopili9 • 10 wrote:

Hi,

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?
rna-seq tool usage transcriptome custom-genome • 472 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by biopili9 • 10
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gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 http://usegalaxy.org. 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 COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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