I received demultiplexed data from my sequence provider with the adaptors and indexes removed, but the primer were still attached to sequence. I would like to remove the primer sequences during the make.contigs command. I previously ran the make.contigs command using a stability.file seen below:
Outfall NI01-Outfall_S1_L001_R1_001.fastq NI01-Outfall_S1_L001_R2_001.fastq
SEDLB NI02-SEBLB_S2_L001_R1_001.fastq NI02-SEBLB_S2_L001_R2_001.fastq
The code ran successfully but my NBases was around 291-300 when it should have been ~250. I know I need to re-run the make.contigs again with an oligos file and have created seen below:
primer GTGCCAGCMGCCGCGGTAA GGACTACHVGGGTWTCTAAT
#BARCODE CGCTCATT ATAGAGGC Outfall
#BARCODE TCCGGAGA ATAGAGGC SEDLB
I have told it to ignore the barcode sequences because they are not supposed to be present.
However when I run mothur >make.contigs(file=stability.files, oligos=testoligos.txt, processors=4), I have a warning that says since I did not provide any group names in the oligos file it is unable to create a group file? I am thinking the group file is likely needed for downstream processing and to keep sequences within their sample grouping. Any advice?