bowtie parameter setting

nunu_ping

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Join Date: Apr 2010

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bowtie parameter setting

09-28-2010, 01:59 PM

I am a beginner in RNA-seq analysis. Which alignment tool is the best one currently? For RNA-seq, should I consider insertion or deletion? If the fragment length of cDNA library is 400-600bp and the sequence data are pair-end, should I set -I to 400 and -X to 600 when using bowtie? Any suggestion on the parameter setting??? Thanks a lot!!
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