You can find the script here. Just install emboss toolkit or make sure you have fuzznuc in your path. Let me know your experience, I will improve it if needed. This script uses given primer sets (reverse and forward) to extract the region which can be amplified. So you can use the primers accordingly. For example, here u can use forward primer fo V3 region and reverse primer for V4.
Usage:- python3.6 extract_n_multiplex.py [options] Options: -h, --help show this help message and exit -f FORWARD_PRIMER forward-primer -r REVERSE_PRIMER reverse-primer -n NITER (default 1) number of iterations to repeat random multiplexing of extracted sequences -d SEQDATA multifasta sequence file from which regions will be extracted.
Dear all, I have got the same problem. I would like to extract all the v3-v4 region from silva.bacteria.fastq file. After consulting to the MISEQ SOP for mothur, I have used the command line as below. But I'm not sure about the start and end position for V3-V4 region. Can someone help to share their experience? Great appreciate for your help.
mothur "#pcr.seqs(fasta=silva.bacteria.fasta, start=6388, end=25319, keepdots=F,processors=8)"