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Old 09-22-2013, 03:12 PM   #1
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Default MiSeq 16S reads (dumb question)


I've got a question that I assume is simple, despite my failed attempts to find the answer online...

I've received some 16s sequences from JGI (MiSeq), and I notice that some sequences in the .fastq file contain a "\1" immediately after the barcode. I assume this means that this sequence only appears once in the dataset, but I cannot find the answer anywhere.

Am I correct in assuming that these sequences are singletons?

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Old 09-22-2013, 06:55 PM   #2
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If you can post an example header then we can be completely certain but in general "/1" generally indicates that the sequence belongs to Read 1 (from a pair in an paired end experiment). See illumina sequence header information in the FASTQ format entry on Wikipedia:
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Old 09-23-2013, 07:06 AM   #3
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Yes, that is exactly what they are. Next time I need to go straight to Wikipedia

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