make.contigs

Commands in mothur
1

Hi,

how do I use these adapter sequences in my oligofile?
I have MiSeq fastq files R1 and R2 and want to make.contigs
and remove the adapter sequences, without loosing nearly
all the sequences to ‘scrap.contigs’.

Left of insert: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
Right of insert: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG

Thanks for help.
Sigmund

2

Here’s a link to mothur’s oligos file, http://www.mothur.org/wiki/Oligos_File.