I tried to run Tophat with different bowtie2 options. I actually used the preset bowtie2 options (i.e. --b2-sensitive). Looking for differences between different runs, i checked the align_summary.txt files for each run and what i got was exactly the same alignment rate. So, i assumed that Tophat aligned the reads with its default options in all cases , ignoring mine. Could anyone help me understand why this happens or experiences the same problem?
Question: Bowtie2 settings in Tophat
5.7 years ago by
zioutisch • 0
zioutisch • 0 wrote:
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