How To Detect Contamination Or Sample Preparation Artifacts In Sequencing Results
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8.7 years ago
roll ▴ 330

Hi,

Is there any tool (apart from fastQC) to detect all primers/adapters(contaminants basically) in my raw fastq file that needs to be removed before mapping?

primer fastq mapping trimming • 3.1k views
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8.7 years ago
arnstrm ★ 1.8k

PRINSEQ gives a nice sequence logo using the FASTQ files like this:

enter image description here

You can easily see any contaminating tags.

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thanks, does this give you statistics or the actual list of contaminants? So that i can use this list to remove them from my data.

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I think the only statistics that it gives is "Probability of tag sequence" at 5' end and 3' end. What kind of list do you need?

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