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Old 01-03-2012, 11:49 AM   #1
Location: VA, USA

Join Date: Oct 2011
Posts: 18
Post Discrepancy in paired-end Illumina data

I have a variety of paired end data sets from Illumina and these are some of their sequence lengths:
Read1 Read2
103 110
103 107
101 101
98 107
Can anyone explain to me, why read1 and read2 have different sequence lengths for some datasets?
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Old 01-03-2012, 11:23 PM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

It's pretty unusual to get this from a standard Illumina run (you can make up a custom recipe to do it though).

Could the samples have had custom barcodes on the front of the first read, which have been stripped before returning the sequence to you?
simonandrews is offline   Reply With Quote

illumina, paired-end, sequence length

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