oligos in make.contigs

Hello,

I got reads from MiSeq and then I am following for the analysis in MiSeq SOP protocol. I understand that fastq in this MiSeq SOP protocol were seperated into each source. However, I have some problem to split barcodes for each source because all sources is pooled within one experiment (like as 454, which I normally use trim.seqs with oligo file in function allfiles=T)

This is the sample in my oligos file :

primer AGAAACGTGAGCGCTG ATACTAGGGTATTTAA
BARCODE ACTATGTG NONE water1
BARCODE TGTACACG NONE water2
BARCODE TACTATGG NONE sand1
BARCODE ATAGCACT NONE sand2
BARCODE AATCGTAG NONE water3

I used command to make contigs and separate oligos in below :

make.contigs(ffastq=POOL_S1_L001_R1_001.fastq, rfastq=POOL_S1_L001_R2_001.fastq, oligos=file.oligos, processors=8)

I got these errors :

Processing POOL_S1_L001_R1_001.0ffastatemp (file 1 of 1) <<<<<
[ERROR]: barcodes must be paired unless you are using an index file.
[ERROR]: barcodes must be paired unless you are using an index file.
[ERROR]: barcodes must be paired unless you are using an index file.

Could you please suggest me?
Thank you very much.
Alisa

Hello,

I tried to use this command :

make.contigs(ffastq=POOL_S1_L001_R1_001.fastq, rfastq=POOL_S1_L001_R2_001.fastq)

After that I got trim.contig.fasta which they combined R1 and R2 together, their barcodes and primers are still appeared in new contigs.
However, I think that I should use trim.seqs from 454 SOP protocol again to trim their barcodes and primers off and split in each source. How do you think about this?

Thank you very much.