SEQanswers Easy question from a noobie
 Register FAQ Members List Calendar Search Today's Posts Mark Forums Read

 Similar Threads Thread Thread Starter Forum Replies Last Post xApple Bioinformatics 5 02-14-2012 09:06 AM lpn RNA Sequencing 1 07-15-2011 06:41 AM m_elena_bioinfo Bioinformatics 0 02-10-2010 08:24 AM GenomeQuest Vendor Forum 0 11-12-2009 08:41 AM

 07-25-2011, 02:22 PM #1 kwatts59 Member   Location: nevada Join Date: Apr 2011 Posts: 46 Easy question from a noobie Can someone please explain figure 2 "Scatterplots of Technical Replicates of Brain Sample" in the paper below? The x and y axis are both labeled the same "Number of aligned reads (log scale), Brain". http://www.illumina.com/Documents/pr...comparison.pdf
 07-26-2011, 04:44 AM #2 HESmith Senior Member   Location: Bethesda MD Join Date: Oct 2009 Posts: 509 Is your question "what is a technical replicate"?
 07-26-2011, 10:29 AM #3 kwatts59 Member   Location: nevada Join Date: Apr 2011 Posts: 46 I think I figured it out. According to the paper, they performed 5 technical replicates on a brain sample. That means they performed the RNA-seq library build and sequencing on the same brain sample five times. So for example, if gene X has the following number of reads that aligned Replicate 1, 152 reads aligned Replicate 2, 127 reads aligned Replicate 3, 98 reads aligned Replicate 4, 173 reads aligned Replicate 5, 111 reads aligned The following 20 points are plotted on the graph (152,127),(152,98),(152,173),(152,111) (127,152),(127,98),(127,173),(127,111) (173,152),(173,127),(173,98),(173,111) (111,152),(111,127),(111,98),(111,173) (98,152),(98,127),(98,173),(98,111) So basically this graph shows that the fewer reads that map to a gene, the less reliable the data.
 07-26-2011, 12:23 PM #4 HESmith Senior Member   Location: Bethesda MD Join Date: Oct 2009 Posts: 509 It looks like a 2D graph, so I'm reasonably certain it's comparing only two of the replicates. Each point represents the read counts for a single gene in the two replicates.