Multiple alignment why and what for (Bowtie -k options)

pmcqt

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Join Date: Mar 2011

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Multiple alignment why and what for (Bowtie -k options)

11-29-2011, 06:48 AM

Hi everyone,

I'm currently discovering the world of RNAseq and trying to run a miRNASeq analysis.

I managed to filter my data on quality and remover adapters...

I am now starting to align my data using bowtie and i read that specific options for miRNA includes the setting of -k to 200. I wonder what is the use of multiple alignment, i would rather keep the best alignment but don't want to wrongly simplify my data.

If i keep multiple alignment, how is it going to be handled by Cufflinks, DESeq or whatsoever in the downstream analysis ?

Any helps or comments will be appreciated

Last edited by pmcqt; 12-02-2011, 12:32 AM.
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