Make.contigs vs trim.seqs

Commands in mothur
1

Hi there,

I have a large HiSeq Illumina data set that needs to be aligned and trimmed to begin with. Before your new release I would align first using make.contigs and then trim the primers and barcodes using trim.seqs. After going over the info page of make.contigs it appears that I now can do this in one step but I am a bit confused as to whether I include the ‘file’ or the ‘oligos’ option. I will have the following information in the file:

primer FWD primer
primer REV primer
barcode xxxxx xxxxx group1
barcode xxxxx xxxxx group2

With a file like this, will make.contigs align AND trim off both paired primers and barcodes. Should I include this file in the ‘file’ or the ‘oligos’ option?

Many thanks!

Claire

2

The make.contigs command can trim paired primers and barcodes with the oligos file, http://www.wiki.mothur.org/wiki/Oligos_File or http://www.wiki.mothur.org/wiki/Make.contigs#oligos. The file option is make.contigs is used for fastq file pairs, http://www.wiki.mothur.org/wiki/Make.contigs#file.

oligos:
primer XXXX XXXXX primerName
barcode xxxxx xxxxx group1
barcode xxxxx xxxxx group2

file:
forward.fastq reverse.fastq

make.contigs(file=myfile, oligos=myoligos)

or

make.contigs(ffastq=forward.fastq, rfastq=reverse.fastq, oligos=myoligos)

The file option is really helpful when you have multiple fastq file pairs you want to process at once.

3

Great, thanks!