Question: Mismatch allowance on Bowtie2 for bacterial RNAseq read mapping
gravatar for l.caetanoantunes
2.9 years ago by
l.caetanoantunes0 wrote:

Hi all, my group has recently performed RNAseq on bacterial samples using Illumina paired-end sequencing. Quality of the runs was ok and we are now trying to analyze the data. However, when we mapped the reads using bowtie2 only 45% of the reads mapped. We do not know why this happened but we suspect that maybe we were too stringent when setting the mismatch threshold at 2. However, I cannot find an article that tells me what a reasonable mismatch cutoff is for this type of experience. Does anyone have a clue? Thanks! Caetano

ADD COMMENTlink written 2.9 years ago by l.caetanoantunes0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1118 users visited in the last hour