Hi,
I have some RNASEQ data from Illumina 1.4+ pipeline.
The barcodes of a multiplex run are appended to the header line of the fastq file. I supposedly have two samples in there, so I am expecting two barcodes, however, I see also many other barcodes different from what I expected. The counts of these "spurious" barcodes is very low, so the majority of the sequences are associated to the expected barcodes.
When splitting the fastq file according to the barcode, how are the sequences with non-matching barcode handled? Do I allow 1 mismach? Do I keep exect matching criteria?
Thanks in advance.
I have some RNASEQ data from Illumina 1.4+ pipeline.
The barcodes of a multiplex run are appended to the header line of the fastq file. I supposedly have two samples in there, so I am expecting two barcodes, however, I see also many other barcodes different from what I expected. The counts of these "spurious" barcodes is very low, so the majority of the sequences are associated to the expected barcodes.
When splitting the fastq file according to the barcode, how are the sequences with non-matching barcode handled? Do I allow 1 mismach? Do I keep exect matching criteria?
Thanks in advance.
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