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Old 10-25-2011, 03:08 PM   #3
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Location: OR, United States

Join Date: Aug 2011
Posts: 5

Hi swbarnes thanks for your reply.

Yes, not knowing the biology behind it, the barcodes are somewhat magical to me (although I suppose a lot of this is). My very rough understanding of it is that we use a specific primer for each different sample and therefore can set our own 3' and 5' "barcodes" or adapters, or whatever else someone might call them. I also should have mentioned this is RNA-Seq stuff, so everything is cDNA.

You're spot on with the illumina "ID" I mentioned being something like lane, title, xy and I am indeed hoping that I can make the assumption that they are from the same DNA fragment if they have the same ID. If they are from the same fragment and one side has a barcode that is correct, I should be able to fix the barcode on the second side and bin it into the correct file.

After I posted this question, a colleague mentioned something about "chimeric molecules". I'm assuming from the PCR step, that would botch up this assumption, but only for a very small % of the reads unless something has gone horribly wrong. Again, I'm very new to all of this and have very little biological background so any info is very helpful.
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