Which Database To Use For Searching Rna-Seq Reads?

Question

[bob-lowlow]

Hi All, I have some RNA-Seq reads and I was wondering which version of blast should I use to search it? e.g. is it tblastx or is there some other database or algorithm to use?? thanks

[Steve Lianoglou]

What are you looking for, exactly?

I mean -- are you looking for enrichment of motif/kmers in your reads or something?

Answer 1

[JC]

None, in general you don't need or want blast for RNAseq analysis -> http://bit.ly/YlbYFz