Mismatch allowance on Bowtie2 for bacterial RNAseq read mapping
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
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