Question: Best Tophat parameters for splicing
gravatar for willtun1991
2.7 years ago by
United Kingdom
willtun199110 wrote:


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?


ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by willtun199110
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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.

Others can offer more help if they want.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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