Hi everyone,
I was recently experimenting with simNGS, the NGS simulation tool of EBI (https://www.ebi.ac.uk/goldman-srv/simNGS/), to create a test dataset for myself. I added a custom adapter sequence to the sequencing setup and ran the simulation. Then when I grepped for the adapter in the produced reads, I see some random nucleotides after the complete adapter sequence at 3' end. I'm wondering how this is possible?
To my knowledge, adapter contamination occurs when the fragment length is shorter than the read length (which I allowed in my simulation), but shouldn't the reaction terminate after going through the complete adapter sequence? Where are those further nucleotides can be possibly coming from? (They are not multiplexed adapters, they are just random as far as I can tell)
Thanks for your replies.
I was recently experimenting with simNGS, the NGS simulation tool of EBI (https://www.ebi.ac.uk/goldman-srv/simNGS/), to create a test dataset for myself. I added a custom adapter sequence to the sequencing setup and ran the simulation. Then when I grepped for the adapter in the produced reads, I see some random nucleotides after the complete adapter sequence at 3' end. I'm wondering how this is possible?
To my knowledge, adapter contamination occurs when the fragment length is shorter than the read length (which I allowed in my simulation), but shouldn't the reaction terminate after going through the complete adapter sequence? Where are those further nucleotides can be possibly coming from? (They are not multiplexed adapters, they are just random as far as I can tell)
Thanks for your replies.
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