Hello! I'm an MD in my background currently running the project on tumour metagenomics. We collected patient samples and analyzed them on Illumina (low microbiological abundance). There is output data uploaded from Illumina. The current issue is as follows: apparently due to the fact that the barcodes were incorrectly specified, the program incorrectly divided the Reads into samples. As a result, almost all sample files are almost empty, and the majority of the information (as concluded by comparing the files size) is stored within the Undetermined.fastq files. I'm trying to extract the information and store it into correct separate files. The problem is that I'm not very experienced in doing that and we are facing troubles while contacting our bioinformatician.
I was proposed to "restart the analyzer program (Illumina MiSeq Reported) and use the correct bards so that the reads are broken down by samples. And, as the next step, analyze the data obtained".
I'm seeking for any advice, as specific as possible. If there is anything I can do by myself, please let me know (I'm familiar with R). Otherwise I would highly appreciate other open-source or paid solution to finally obtain the results. We've done huge amount of work collecting those samples and I feel frustrated to loose it.
Any advice is appreciated. Best regards.