GC content bias in ATCC mock reads

ciemanek · 11-06-2019, 01:29 AM

Hi! I have samples sequenced with NextSeq for the experiment protocol setup. We tested different kits (Nextera, Kapa, Qiagen) and apart from the donor samples, we sequenced ATCC bacterial mix with the addition of human cells, as well as ATCC genomic DNA. What I observe in QC reports is first of all, per base sequence content bias, but also disturbing GC content distributions for ATCC samples (yellow ones are the bacterial mix, the red one is genomic DNA). Would that suggest contamination or some other issue, or could it be a characteristic of those samples?

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11-06-2019, 01:29 AM	#1
ciemanek Junior Member Location: Cracov, PL Join Date: Jul 2019 Posts: 5	GC content bias in ATCC mock reads Hi! I have samples sequenced with NextSeq for the experiment protocol setup. We tested different kits (Nextera, Kapa, Qiagen) and apart from the donor samples, we sequenced ATCC bacterial mix with the addition of human cells, as well as ATCC genomic DNA. What I observe in QC reports is first of all, per base sequence content bias, but also disturbing GC content distributions for ATCC samples (yellow ones are the bacterial mix, the red one is genomic DNA). Would that suggest contamination or some other issue, or could it be a characteristic of those samples?