Bowtie2 orientation mapping question

Question

[Andrés Ribone]

Hi, I have a little question about how Bowtie2 works.

I have a dataset of Illumina paired-end strand-specific reads. I assembled it de novo using Trinity, and now I'm assessing its quality using several metrics.

One of them is aligning the initial reads with the new contigs. For that I'm using Bowtie2; but I wonder: Given a forward read and a contig, does Bowtie2 try to align the read in both strands? I always assumed that the answer is yes, but just to be sure.

Thanks!

Answer 1

[Devon Ryan]

Yes, bowtie2 will attempt to align the pair of reads in both orientations.