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Old 02-14-2014, 04:48 AM   #1
Location: Enschede

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Default Bowtie2 - Own Indexes

I was wondering... perhaps it's a really stupid question but ok. I've got +- 100 control sequences, is it possible to build an own '6 indexes (bt2)' out of that via the bowtie2-build. So that I'm able to map all my RNAseq sequences against these controls?

And if so, what parameters should I use? Because I know used -hg19 for the genome indexes.
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Old 02-14-2014, 04:54 AM   #2
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Keep the order of command line options as indicated on the help page.
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