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Question: Reference Annotation For Whole Transcriptome Rna-Seq
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gravatar for Davide Degli Esposti
5.8 years ago by
Davide Degli Esposti • 80
Davide Degli Esposti • 80 wrote:
Dear all, I am trying to get an exhaustive reference annotation for RNA-Seq analysis. I was thinking that the patched GTF annotation files for cufflinks Jeremy indicates in RNA-Seq step by step tutorial should be fine for me, but I am not able to find on the Shared data > Data libraries. Have they been replaced by iGenomes annotations? I thank you for your help Best regards Davide---------------------------------------------------------------- ------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use
rna-seq cufflinks • 1.3k views
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modified 5.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.8 years ago by Davide Degli Esposti • 80
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gravatar for Jennifer Hillman Jackson
5.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Davide, Yes, if the iGenomes annotation data collection includes a reference GTF dataset for your genome, that would be the best choice, as it would include all of the attributes that the RNA-seq tools (Cufflinks, CuffDiff, etc) require for full functionality. The hg19 and mm9 GTF files are on the public Main Galaxy instance Shared Library "iGenomes". The complete set is located at the Cufflinks web site here: http://cufflinks.cbcb.umd.edu/igenomes.html The RNA-seq tutorial also uses the iGenomes dataset - so perhaps you are referring to the prior version, or possibly the FAQ that provides help with converting formats (may be necessary if an iGenomes dataset is not available for a particular target genome)? In any case, latest tutorial is located here and represents the most current 'best practice' guidelines we have for this tool set: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.8 years ago by Jennifer Hillman Jackson ♦ 25k
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