Question: Bowtie2 orientation mapping question
0
gravatar for Andrés Ribone
2.3 years ago by
Andrés Ribone0 wrote:

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!

ADD COMMENTlink modified 2.3 years ago by Devon Ryan93k • written 2.3 years ago by Andrés Ribone0
2
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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

ADD COMMENTlink written 2.3 years ago by Devon Ryan93k
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