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…
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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?
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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.