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Old 01-30-2013, 05:38 AM   #1
Seq_g
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Default Read length of different illumina machines

Dear All,
I was wondering about the read length of different illumina instruments like:

Illumina GAIIx read length of 150+150
Illumina HiSeq read length of 100+100

But I also had paired/single end reads ( not mate pairs for sure) with a read length of 27-36, Does anyone knows which illumina machines produced those ?

Cheers,
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Old 01-30-2013, 05:53 AM   #2
GenoMax
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Quote:
Originally Posted by Seq_g View Post
Dear All,
I was wondering about the read length of different illumina instruments like:

Illumina GAIIx read length of 150+150
Illumina HiSeq read length of 100+100

But I also had paired/single end reads ( not mate pairs for sure) with a read length of 27-36, Does anyone knows which illumina machines produced those ?

Cheers,
GAIIx maxed out at 76 bp reads in our hands. 36 bp runs were the norm early on. We also ran 50 bp.

HiSeq runs can be of varying length. In general, SE/PE/Multiplex 50bp to 150bp (on the HiSeq 2500 variant) would be common lengths at this time.

It would be difficult to know for sure but the reads you describe (27-36) could possibly have come from a GAII or GAIIx, specially if they are not of a recent vintage.
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Old 01-30-2013, 05:56 AM   #3
mcnelson.phd
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The GA, HiSeq, and MiSeq can all give you those 27-36 bp reads, but most likely it's GA or early HiSeq data. You should be able to roughly tell what machine was used from the sequence ID in the fastq file. I can't say for sure that it was always like this, but all current fastq files from Illumina instruments incorporate the sequencer's serial number in the ID

To give an example, for files coming off our MiSeq the sequence IDs all begin with @Mxxxxx. The M indicates the instrument is a MiSeq, and the serial # is the xxxxx. HiSeqs are HWI if I'm remembering this off the top of my head correctly.
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Old 01-30-2013, 10:18 AM   #4
kcchan
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Originally Posted by mcnelson.phd View Post
The GA, HiSeq, and MiSeq can all give you those 27-36 bp reads, but most likely it's GA or early HiSeq data. You should be able to roughly tell what machine was used from the sequence ID in the fastq file. I can't say for sure that it was always like this, but all current fastq files from Illumina instruments incorporate the sequencer's serial number in the ID

To give an example, for files coming off our MiSeq the sequence IDs all begin with @Mxxxxx. The M indicates the instrument is a MiSeq, and the serial # is the xxxxx. HiSeqs are HWI if I'm remembering this off the top of my head correctly.
You're correct. HiSeq read headers start off with @HWI-ST, while GA reads start with @HWUSI-EAS. These names refer to the fact that the instrument was built in Hayward, CA as well as the codename used during development.
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Old 01-30-2013, 10:28 AM   #5
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Thank you every one. Your reply's helped me
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