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Old 01-16-2015, 11:02 AM   #1
Location: Philadelphia, PA

Join Date: Dec 2009
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Default MiSeq FastQ Header for pair-end data

So the Miseq fastq header for pair-end data has changed. I used to see a /1 or /2 at the end of the read name. Now I get something like this for the first read:

@HWI:1:X:2:1101:1094:2143 1:N:0: CGGCTATG-ATAGAGGC

and this for the second read:

@HWI:1:X:2:1101:1094:2143 4:N:0: CGGCTATG-ATAGAGGC

I've seen the the number 3 or 4 in the second read but not sure what they mean, and haven't seen an explanation anywhere. Does anyone know what this number signifies?
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Old 01-16-2015, 11:41 AM   #2
Brian Bushnell
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That's good to know; I had only seen 2 for read 2 - now I need to update my header-detection routines. I imagine it has to do with how the machine counts sequencing phases for dual-index:

1: Read 1
2: Barcode 1
3: Barcode 2
4: Read 2

It's not unusual for Illumina to randomly change stuff like that with software updates, which is pretty annoying.
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Old 01-16-2015, 12:49 PM   #3
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Can you tell us where the data was analyzed, on instrument/in BaseSpace? Was the analysis done using standard parameters (i.e. no separate fastq files for tag reads).
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Old 01-16-2015, 03:06 PM   #4
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If the headers are starting with @HWI it's almost certainly generated using BCL2FASTQ and not MiSeq Reporter, which uses @M0xxxx.
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