using BBmap to map paire end reads to de-novo assembled transcriptome

Question

[rahmati.razieh83]

Dear all

I received some RNA seq reads containing Lexogen primers. My reads do not have any refrence genome. Because of existing primers in the reads, mapping my reads by TopHat to assembled transcriptome will reduce the mapping rate significantly. Regarding having no reference genome, Can I map my reads by BBmap to assembled transcriptome provided by Trinity? Dose BBmap need to reference genome for mapping?

Answer 1

[GenoMax]

If you are going to align then you will need a reference no matter what genome you are working with. You can use trinity assembled transcriptome as a reference with BBMap. There are other aligners like GMAP that may be useful for this as well.

[rahmati.razieh83]

Thank you so much for your comment