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Question: Best Tophat parameters for splicing
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gravatar for willtun1991
2.7 years ago by
willtun1991 • 10
United Kingdom
willtun1991 • 10 wrote:

Hey

I was wondering if there are any key parameters to consider for Tophat to maximise my chances of accurately finding splice events when I align my pair-end illumina reads with my human Hg38 reference genome?

Can anyone recommend good parameters for this task?

Will
rna-seq tophat alignment parameters splicing • 676 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.7 years ago by willtun1991 • 10
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Including reference annotation can help (to make sure that known splices are captured). This option is under TopHat settings to use: Full parameters: Do you want to supply your own junction data? Yes. There are a few ways to set this, maybe try a few to see which works best with your data/goals and decide.

For hg38, iGenomes has a reference GTF that would be a good choice to use, for this tool and others downstream in the Tuxedo RNA-seq analysis pathway. Download the hg38 tar file, unpack it, then load just the genes.gtf file up into Galaxy for use.

http://support.illumina.com/sequencing/sequencing_software/igenome.html http://cole-trapnell-lab.github.io/cufflinks/manual/

Others can offer more help if they want.

Best, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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