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Old 11-14-2018, 10:56 PM   #5
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,234

Stretches of G in NextSeq indicates lack of signal in those cycles and it could be result of short inserts and adapter-dimer.

In a shot gun library GC content peak will be representative of genome GC but IP pull down is not random and some bias is expected depending on what sequences are pulled down and enriched.

From FastQC manual:

"This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content."

"An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be."
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