Question about optimum parameters

[Zoe Ward]

Hi Alex,

I have been running my data with the parameters that are in the manual which are the ones optimised for lncRNA.

Which parameters would you change if you're dealing solely with mRNA??

Thanks,

Zoe.

[Alexander Dobin]

Hi Zoe,

I would not say that the parameters in the manual are optimized for lncRNA - they are generally good for long RNA-seq in mammals.

Cheers

Alex