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Old 06-12-2018, 10:26 PM   #1
Location: Germany

Join Date: Apr 2018
Posts: 11
Default FastQC warnings


using FastQC I always get one error and two warnings for each of my samples (bacterial samples, WGS).

per base sequence conent
--> here, I assume that tagmentation is the reason - so I can ignore this error warning. Someone told me that Illumina data usually fail here due to the fact that tagmentation is not as random as previously supposed

Warnings (se figures)

1. Sequence Length Distribution
2. Sequence Duplication Levels

Is this something to worry about? Why do I get warnings here?
Attached Files
File Type: pdf FastQC.pdf (139.6 KB, 20 views)
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Old 06-13-2018, 02:10 AM   #2
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,196

Sequence length distribution: it seems to be the result of trimming adapters

Duplication Levels: deep sequencing in relation to library diversity

per base sequence content: could be result of tagmentation but you have not posted this plot
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Old 06-14-2018, 01:56 PM   #3
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Location: Purdue University, West Lafayette, Indiana

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Neither of these warnings are worrisome.
BTW, a 4 million base pair genome provides only 8 million possible places to start a sequence read. Any more reads that that and you will certainly have duplications.

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Old 06-15-2018, 04:27 AM   #4
Location: Germany

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Thank you for your answers!
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