Determining paired end sequences

General Discussion
1

Hi all, is it possible to tell which paired end barcodes were used on a sample in the fastq file?

For example, will it effect the analysis if you list the paired end barcodes wrong in the metadata or get one or two of them mixed up?

Best wishes

2

Hi everyone, is it possible to tell which paired end barcodes were used on a sample in the fastq file?
Can you look at a fastq and know what barcodes are attached or does it not matter?

For example, will it effect the analysis if you list the paired end barcodes wrong in the metadata or get one or two of them mixed up?

Best wishes

3

Hi @Mantella86,
I'm not certain that I follow your question. Could you perhaps provide some examples of the files you're working with to help?

It is likely very important though to understand the barcoding scheme that was used perfectly. Otherwise you could end up losing some reads that you could otherwise retain, or worse, mixing up the relationship between sample identifiers and the sequences that were observed in that sample.