Hi Clayton, Galaxy (http://main.g2.bx.psu.edu/) has some tools that you are interested in. They have some GTF/GFF tools under the "Filter and Sort" menu. If you have questions about these tools you will need to contact them: [email protected].
If you are interested in using data from our site you can use the table browser to extract it. Here is a previously answered mailing list question that will give you an example on how to go about that: https://lists.soe.ucsc.edu/pipermail/genome/2010-November/024058.html Another way that you can go about this is upload your data as a custom track and then using the table browser to extract the data. To get to the custom track upload page you will need to click on "Genomes" from the blue navigation bar and then click on "add custom tracks". Please take a look at the user's guide: http://genome.ucsc.edu/goldenPath/help/customTrack.html and there is a help document on the GTF format: http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF. Once you have uploaded the track you can select that as a track in the table browser which you can get to by clicking "Tables" from the blue navigation bar. There is a link to a User's guide a link to tutorial on that page if you need additional help. Hope that leads you in the right direction. If you have further questions about the Genome Browser, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Clayton K Collings <[email protected]> Date: Sun, Nov 27, 2011 at 7:41 AM Subject: [Genome] filtering rRNA out of GTF files To: [email protected] Hello genome browsers, Does anyone know how to filter rRNA out of a GTF file? I would also really like to know how to obtain a GTF file with only rRNA. What I really need is a complete list of gene ids - like the ones that appear in the GTF file that correspond to rRNA. For a class project, I am using RSEM to map and count reads per gene with multiple RNA-seq datasets and then comparing differential expression results between DESeq and EdgeR. I believe that the rRNA and possibly the mtDNA genes are negatively affecting my gene expression results due to excessive coverage. I basically want to filter my RSEM results to exclude genes with IDs that correspond to rRNA. By the way, RSEM uses Bowtie to prepare a transcriptome reference sequence and map reads. To prepare the transcriptome reference sequence, one must input the GTF file along with the entire human genome. I am pretty sure that I can figure out how to filter the mtDNA genes as that just requires filtering out an entire chromosome. Thanks for your time. Sincerely, Clayton _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
