I consider myself a novice NGS and Mothur user. So while I understand some things, other things i may not understand deeply. Please bear with me.
I received my data set from LC Sciences, I was expecting a 2 x 250 of the v3-v4. What I received was two sets of data one of the typical R1 and R2 raw files, but no barcodes or adaptor key. The other dataset is a “cleaned” contig resulting from making a contig of R1 and R2.
I have inquired about getting the barcode/adaptor key so I can use make.contigs (), I have not received that yet, but they told me to use the cleaned contigs in my analysis.
Upon looking into the cleaned contigs they are ~400 nuc long, while the R1 and R2 are 250 nuc long. I can manually align the R1 and R2, and they form the contig of 400 nuc, with overhangs and a overlap of 20-30 nuc. Though the R1 and R2 contain extra information that the cleaned version does not have.
r1 - CNTACGGGGGGCTGCAG
r2 - GGATTAGATACCCCAGTAGTCGA
So right now I do not think I can use the make.contig command without a key to remove these extra bits of information from my 3.8 million seq data set of raw R1 and R2. Currently I do not know of any mothur command where I can enter the cleaned contigs, so I can match to SILVA for analysis.
If understand my problem here, I need the barcode key to proceed correct? because there is not much i can do with the cleaned contigs?