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Old 01-20-2014, 04:25 AM   #4
benjaminsb
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Location: Oxford

Join Date: Aug 2013
Posts: 2
Default Similar problem

I've just run FastQC on a published RNAseq dataset (SRX294957) and I see a very similar pattern:



where on position 21-23, 80% of reads are N's. As I'm only interested in expression, I could accept the low read quality as long as the aligner accepts it. I'm using RSEM+bowtie for the purpose, so I'm wondering if bowtie will match NNN against anything in the reference?
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