I am trying to stitch my paried end illumina reads. I am able to do it with the fastq format input, however i received only a fastq file from my sequencing facility and not an additional/separate barcodes file. When I receive the output from make.contigs it is only a fasta file, which no longer seems to contain the information I need to demultiplex the reads. Should I be demultiplexing the sequences before make.contigs or is there a way to do it afterward?
I’m not sure what sequencing strategy you are following…
If you are sequencing across the barcodes / primers, then you sequencing facility has to give you the information. If not, ask for your money back - how are you supposed to know what reads correspond to each sample?
If you are following something like we are doing in the AEM paper, then your sequencer should generate separate fastq files for each read and sample. A run for 96 samples should generate 192 files. With this strategy, the reads do not have the barcodes or primers and the group file is generated in the make.contigs file.