Hello to everyone.
I have two types of question. One related to the statistical analyses and the other one is more about genomics.
I have 48 demultiplexed paired end sequences some of them treated and some not.
I want to analyze them to find out the differences between varieties, locations and other variables. In the normal situation when I have some variables I can easily analyze the data because I have some values (integers), compare the means and etc (Like ANOVA). But in the case of having paired-end sequences (FASTQ files) I don’t know what the normal way is to do the procedure.
I would appreciate it if you can give me some guides, please.
I also attached some of the data (In three continues images).
My second question:
How to find out “LinkerPrimerSequence” or “BarcodeSequence” ? Furthermore, how can I obtain the BarcodeSequence?
Other relevant information:
Following primer sequences were used 16S-341F 5’-CCTACGGGNGGCWGCAG-3’ 16S-805R 5’-GACTACHVGGGTATCTAATCC-3’ for the 16S locus.
Libraries were sequenced on MiSeq instrument (Illumina, San Diego, CA) using 300-bp paired-end.