Question: TopHat alignment of RNA seq data
gravatar for Diana Afonso
2.2 years ago by
Diana Afonso10
Diana Afonso10 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

ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.2 years ago by Diana Afonso10
gravatar for VY
2.2 years ago by
VY120 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 COMMENTlink written 2.2 years ago by VY120
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan1.9k
Devon Ryan1.9k 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 COMMENTlink written 2.2 years ago by Devon Ryan1.9k
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