I am stuck in the 454 SOP to analyse my 454 data. My previous post disappeared somehow from this forum but I really hope someone could see what I am doing wrong.
mothur > sffinfo(sff=HD13.sff, flow=T)
Extracting info from HD13.sff …
It took 17 secs to extract 18736.
Output File Names:
mothur > trim.flows(flow=HD13.flow, oligos= primerseq.oligos, order=B)
bash: syntax error near unexpected token `flow=HD13.flow,’
My oligos file looks like this:
- forward ATTAGATACCCNGGTAG vF
reverse ACGGGCGGTGWGTRC vR
No barcodes are needed since I have already demultiplexed data. The pool.trim.flow file has as its first line “450”. Let me know If you need more information.
Any help is welcome