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

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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?
Thanks,
Vishal
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Old 01-03-2012, 11:23 PM   #2
simonandrews
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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?
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