We've had some odd trimming results and I thought I'd check whether anybody else has had a similar experience.
I received raw 454 reads from our provider with the A & B adapters removed (presumably via the 454 pipeline). I have MIDs on both the 5' and 3' end of the reads to facilitate multiplexing. I've noticed, however, that reads with MID 16, 18, 19, and 22 on the 3' end of the read have their terminal (i.e. 3') T nucleotide missing. Depending on how you demultiplex, this can mean that MIDs are not correctly read & sorted. The problem seems restricted to the MIDs I've used that begin with T
It seems something to do with trimming the B adapter because MIDs that I have on the 5' end of the read, such as MID 10 that also have a terminal T (i.e. 5'), retain the T.
Anybody else come across this?
I received raw 454 reads from our provider with the A & B adapters removed (presumably via the 454 pipeline). I have MIDs on both the 5' and 3' end of the reads to facilitate multiplexing. I've noticed, however, that reads with MID 16, 18, 19, and 22 on the 3' end of the read have their terminal (i.e. 3') T nucleotide missing. Depending on how you demultiplex, this can mean that MIDs are not correctly read & sorted. The problem seems restricted to the MIDs I've used that begin with T
It seems something to do with trimming the B adapter because MIDs that I have on the 5' end of the read, such as MID 10 that also have a terminal T (i.e. 5'), retain the T.
Anybody else come across this?
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