I'm a newbie in bioinformatics and with QIIME pipeline.
I received 16S rRNA amplicon sequencing data from Illumina MiSeq. 16S rRNA amplicons were sequenced from both ends - paired end sequencing. Among the different folders that i received, from the core sequencing facility, it was a "raw" folder. This contain individual fastq files for each end (forward and reverse) and for each sample (9 in total). So, the fastq files that i received were already demultiplexed, without barcodes, but with primers.
My questions are:
(1) How do i start? By merging the files and then removing the primers or the opposite?
(2) How do i perform any script that requires the "map.file" if i don't know the barcode sequences?
(3) How do i can perform downstream analysis, such as beta and alpha diversity, without map.file?
I started by running the
multiple_join_paired_ends.py script. Now i'll try merge all the samples (9) in just one fastq file. Then i was thinking to remove both primer sequences, forward and reverse, through
extract_barcode.py using the following argument
Please, help me. This is really frustrating for someone that just started to learn about bioinformatics and pipelines like QIIME without previous experience on that. Regards, @renh@