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Question: TopHat alignment of RNA seq data
1
gravatar for Diana Afonso
2.2 years ago by
Diana Afonso • 10
Portugal/Braga/ICVS
Diana Afonso • 10 wrote:

Hello everyone,

I want to use TopHat trough Galaxy to perform the alignment of single end RNA Seq data. I would like to know if usually you use the default settings or if you determine specific parameters according to the analysis you intend to do.

Thank you. Diana Afonso
hiseq tophat alignment parameters rna-seq • 969 views
ADD COMMENT • link •
modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by Diana Afonso • 10
1
gravatar for VY
2.2 years ago by
VY • 120
London
VY • 120 wrote:

Hi Diana,

As everything you can't really let the tools run on autopilot without knowing what it is you're doing or why. My suggestion would be read the documentation and actually get a feel about what each parameter does. If you're pushed for time to get some results or need to confirm a hypothesis you have I would suggest using HISAT2 on galaxy. It's far less fiddly with less things to play around with and much faster. You can then do your analysis downstream using DEseq2. TopHat might take abit longer to optimise but ideally should give you more or less the same results at the end.

Hope that helps, Val
ADD COMMENT • link written 2.2 years ago by VY • 120
1
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Use the defaults, which is the first thing to do with all tools. Then have a look at the results and see if they seem reasonable. If so, you're done. If not, you might need to tweak some settings.
ADD COMMENT • link written 2.2 years ago by Devon Ryan • 1.9k
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