I have data from an RNA-seq experiment on the SOLiD platform.
One round of Ribominus was used before library preparation to get rid if rRNA.
I want to assess how well this process worked.
Using bowtie I made an index of all the rRNA sequences I could find (in mouse) and aligned against it. Result was 10-11% of my reads mapped to rRNA.
I also mapped my reads to the entire genome obtained in colorspace format from bowtie's website.
My question is does the genome index include the rRNA sequences? Should I subtract the 10-11% from my mapped reads?
Thanks.
One round of Ribominus was used before library preparation to get rid if rRNA.
I want to assess how well this process worked.
Using bowtie I made an index of all the rRNA sequences I could find (in mouse) and aligned against it. Result was 10-11% of my reads mapped to rRNA.
I also mapped my reads to the entire genome obtained in colorspace format from bowtie's website.
My question is does the genome index include the rRNA sequences? Should I subtract the 10-11% from my mapped reads?
Thanks.
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