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Old 10-13-2010, 12:28 AM   #7
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

I'm not sure the Illumina pipeline can create unpaired reads. The basis for the sequencing is an initial identification of regions followed by tracking those regions to determine sequence. When you do a paired end read there is no separate cluster detection in the second read, meaning that you use exactly the same regions as the first read.

For the output from the pipeline you get only two sequence files, one for each read, which always contain the same number of sequences and always come in the same order so you can match up pairs of sequences. If stuff goes wrong you'll just end up with a bunch of sequences full of poly-N.

If the file is for unpaired sequences then it must have been something which the researchers created from the original data, as the pipeline itself won't create this.

Could it be a trial run before the main sequencing run? We do this routinely with our libraries - doing 10% of a lane with them to see if they look OK before going on to do a full run.
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