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Question: How Insert Gene Ids?
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gravatar for Asuncion Lago
7.8 years ago by
Asuncion Lago • 20
Asuncion Lago • 20 wrote:
Hi, I have used the RNAseq tools to calculate the FPKMs values, now I would like to know how I can link this values with the gene name or the Flybase ID in my particular case. I have been trying in different ways without success. Could you help me, please? A El 17/12/10 16:57, "galaxy-user-bounces@lists.bx.psu.edu" <galaxy-user-bounces@lists.bx.psu.edu> escribió:
galaxy • 900 views
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modified 7.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.8 years ago by Asuncion Lago • 20
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gravatar for Jennifer Hillman Jackson
7.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Asuncion, FlyBase genes can be imported to Galaxy using "Get Data -> UCSC Main table browser". To join in the annotation with your data, use BED format with the "Operate on Genomic Intervals" tools or use GTF with the "NGS: RNA Analysis" tools. Please note that the data from UCSC is not from the most current FlyBase release. Here is a history where I imported the data as an example and annotated the date: http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/dm3-flybase-genes Another choice is to obtain the most current release of Flybase directly from the source at: ftp://ftp.flybase.net/releases/FB2011_01/dmel_r5.33/gff/ Please note that the release data at Flybase will require a bit of tuning before use. The general path would be to ftp the data locally, modify the files, then upload into Galaxy. Specifically, you will want to adjust the chromosome names to be in the exact format as in Galaxy's native dm3 assembly (see the chromInfo file, dataset #3 in the shared history above). Some filtering of the release will also be necessary to limit the content to gene annotations only (if desired). And as the files are in GFF format (specifically GFF3), not GTF, that will need to be adjusted as well, unless you want to use BED format. If BED format is the goal, then you can just "Get Data -> FTP" the GFF data into Galaxy and using the tool "Convert Formats -> GFF-to-BED" should be possible. Best wishes with your research and please let us know if we can help again, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k
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