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?
PRINSEQ gives a nice sequence logo using the FASTQ files like this:
You can easily see any contaminating tags.
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.
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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