Starting with already demultiplexed data
I'm having some trouble figuring out how to start with data that has already been demultiplexed. The data I have has already been split into fastq files for each sample, with the illumina and sample specific tags already removed. I've spent some time with the tutorial data and my own data using the obi tools but can't quite figure out the best way to hop into the pipeline. My specific questions would be:
Should I start at the inital import and simply skip over the ngsfilter step and if so, do I need to manually add tags to the DMS that would be added by ngsfilter and that are needed later?
Is there a way to merge the samples so they are all analyzed at once as they would have been if they started multiplexed or is doing them each individually the only option?
An additional complication is that within each demultiplexed sample are up to 3 different primer pairs.
Are the forward and reverse primer annotations that are added by ngsfilter needed in the downstream analyses?
Does each primer pair need to be used in ecopcr separately or can/should they be somehow run together?
Thanks in advance for your response, and I look forward to using what seems to be a great tool.