Expected Transcriptome Blast

Question: Expected Transcriptome Blast

7.1 years ago by

Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus. The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against. I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file. Thanks, Jack

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modified 7.1 years ago • written 7.1 years ago by Colicchio, Jack M • 20

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, To use a custom genome with the alignment tools at Galaxy Main (http://usegalaxy.org), the dataset must be in fasta format. If the data is RNA, then using the tools in "NGS: RNA Analysis" will accept both a reference custom genome and a transcript file in GTF format to guide placement (using TopHat as the preferred alignment tool). It is important to note that the Main Galaxy site does not offer a BLAST option (with the exception of Megablast against a specific set of genomes), but a local or cloud instance would, using the BLAST tools in the tool shed and setting up your own data. Some help links: If using the RNA Analysis tools at Galaxy Main: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP If using a local or cloud instance: http://getgalaxy.org http://galaxyproject.org/wiki/Admin/Cloud http://galaxyproject.org/wiki/Tool%20Shed Hopefully this offers you a choice that will work for your project, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

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Colicchio, Jack M • 20

Colicchio, Jack M • 20 wrote:

Also, I'm working under John Kelly and Lena Hileman at KU. We, along with our collaborators at Duke, would get a lot of use out of an expected transcriptome that we could blast illumine data against. If we sent you our genome in .fasta format along with the .gff expected transcript file is their anyway you could combine these into a database we could align against? -Jack

ADD COMMENT • link written 7.1 years ago by Colicchio, Jack M • 20

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