sequencing/NxTrim

Mate pair SamplePrep V2

Closed this issue · 4 comments

kokyriakidis commented

Hi! Does it also work for non-Nextera MATE PAIR libraries such as Mate pair SamplePrep V2? They also have internal biotinylated adapters and are in RF orientation! Does NxTrim work in this case?

jaredo commented

I think these older kits do not have the junction adapter and hence would not need this sort of trimming.

@olest do you know the answer to this?

olest commented

Yes, I think the V2 mate pairs don't have the adapter . You could check if your library contains it, the sequence is given here : https://github.com/sequencing/NxTrim/blob/master/docs/adapter_matching.md

kokyriakidis commented

Yes, they do not have the adapter. So NxTrim cannot distinguish them into Mate pair, PE, unknown and SE? Should I do any extra prepossessing step apart from adapter trimming error-correction etc?

jaredo commented

So NxTrim cannot distinguish them into Mate pair, PE, unknown and SE?

That is right, NxTrim is not appropriate for these data.

Should I do any extra prepossessing step apart from adapter trimming error-correction etc?

I have not used these libraries before, but your suggestions sound correct.