MiSeq FastQ Header for pair-end data

golharam · 01-16-2015, 11:02 AM

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?

Brian Bushnell · 01-16-2015, 11:41 AM

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.

GenoMax · 01-16-2015, 12:49 PM

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).

kcchan · 01-16-2015, 03:06 PM

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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01-16-2015, 11:02 AM	#1
golharam Member Location: Philadelphia, PA Join Date: Dec 2009 Posts: 55	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?

01-16-2015, 11:41 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.

01-16-2015, 12:49 PM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,082	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).

01-16-2015, 03:06 PM	#4
kcchan Senior Member Location: USA Join Date: Jul 2012 Posts: 184	If the headers are starting with @HWI it's almost certainly generated using BCL2FASTQ and not MiSeq Reporter, which uses @M0xxxx.