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Old 01-07-2014, 11:07 PM   #1
themysticgeek
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Location: India

Join Date: Dec 2013
Posts: 4
Question How to handle Ns in the middle of reads

For my illumina data fastqc shows presence of N's at positions 13,14,15 in 101 bp longs reads. If i go for cropping first 15 bases by using trimmomatic, it solves the problem but i lose a lot of data. I wanted to know that if i retain the N's what sort of problems would they cause during alignment(bwa+stampy)/variant calling(unified genotyper) and how can i handle these problems?

If any body faced a similar problem how did you handle it? Similar questions asked on different forums but none answered. Could not find a resourse on how variant calling programs handle N's. Do they ignore them? Or consider them as a variation with low confidence scores?

Last edited by themysticgeek; 01-08-2014 at 01:55 AM.
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