Make.contigs vs trim.seqs

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!


The make.contigs command can trim paired primers and barcodes with the oligos file, or The file option is make.contigs is used for fastq file pairs,

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

forward.fastq reverse.fastq

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


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.

Great, thanks!