Mapping rate with PolyA and Ribo-zero selection on NextSeq 500 and HiSeq 4000

Jane M

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Join Date: Aug 2011

Posts: 239
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05-09-2016, 05:15 AM

Still interested in your percentages of remaining rDNA sequence after ribodepletion

I have one more question concerning what are the unmapped reads in the ribodepleted experiments. When looking at the overall mapping rate to hg19 and the overall mapping rate to rDNA for my 4 samples, one can see that Mapping Rate to hg19 + Mapping Rate to rDNA is beyond 100%:

Code:

Sample MappingRateTohg19 MappingRateTorDNA Sample 1 79.8 24.3 Sample 2 88.2 14.1 Sample 3 84.7 18.1 Sample 4 87.8 13.3

What are those reads common to hg19 and rDNA: multimapped reads? rDNA sequences included in hg19 (Human ribosomal DNA complete repeating unit - http://www.ncbi.nlm.nih.gov/nuccore/U13369.1 - contains ~43kb. Isn't it too large)? Any feedback?

Thank you

Last edited by Jane M; 05-09-2016, 07:35 AM.
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