Hi all,
I have the following problem:
I have a dataset containing circurlarized and linear DNA. It was amplified with two pairs of primers using inverse PCR. I'd like to dissect the data by the following scheme:
Primer1a----------Primer1b
Primer2a----------Primer2b
Primer1a---------- or ----------Primer1a
Primer1b---------- or ----------Primer1b
Primer2a---------- or ----------Primer2a
Primer2b---------- or ----------Primer2b
I tried to use cutadapt for this issue, but it seems that for the paired primers I only get the sequences with e.g. 1a at 5', 1b at 3' and have to specify it the other way around.
cutadapt -g ^P1 -a P2\$ --trimmed-only -e 0.05 --no-trim >out.fasta in.fasta
I need an approach where I can specify a certain error rate as well as the possibility to search for example within the first and last 40 bp for my 20 bp primer.
Do you have any suggestions???
Thanks in advance!
I have the following problem:
I have a dataset containing circurlarized and linear DNA. It was amplified with two pairs of primers using inverse PCR. I'd like to dissect the data by the following scheme:
Primer1a----------Primer1b
Primer2a----------Primer2b
Primer1a---------- or ----------Primer1a
Primer1b---------- or ----------Primer1b
Primer2a---------- or ----------Primer2a
Primer2b---------- or ----------Primer2b
I tried to use cutadapt for this issue, but it seems that for the paired primers I only get the sequences with e.g. 1a at 5', 1b at 3' and have to specify it the other way around.
cutadapt -g ^P1 -a P2\$ --trimmed-only -e 0.05 --no-trim >out.fasta in.fasta
I need an approach where I can specify a certain error rate as well as the possibility to search for example within the first and last 40 bp for my 20 bp primer.
Do you have any suggestions???
Thanks in advance!
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