Kun:LabNotes/SingleCellExpr/2013-8-14

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Revision as of 17:50, 14 August 2013 by KunZhang (talk | contribs) (Created page with "==HL157 run data analysis== *Rui&Blue make eight libraries from single mNPCs using various protocols. *The libraries were sequenced on a PE flowcell. *There were no reads in L...")
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HL157 run data analysis

  • Rui&Blue make eight libraries from single mNPCs using various protocols.
  • The libraries were sequenced on a PE flowcell.
  • There were no reads in Lane 6-8 (three IVT libraries made by Rui).
  • The other IVT library made by Rui has 33 million reads in Lane 5. However, most reads came from the N6 primer annealing on the T20 primer, there was no insert.
  • The following analysis focused on Lane 1-4. Because the read numbers were not high, I did not split each data file into single cells. Instead I treated the pooled libraries as individual data sets to get a quick idea on the quality of the libraries.
Data set # raw reads # UMI/GGG reads Template switching accuracy # unique reads (MQ>20) # unique/non-clonal reads # ERCC reads # unique ERCC reads '
s_1_1_Indx14.txt 29,228,570 26,331,150 90.1% 1,873,037.0 952,715.0 4,184.0 822.0 0.196462715
s_2_1_Indx15.txt 25,678,289 18,851,465 73.4% 1,311,840.0 718,991.0 1,727.0 569.0 0.329473075
s_3_1_Indx81.txt 12,930,738 5,474,853 42.3% 1,096,219.0 223,910.0 214.0 87.0 0.406542056
s_4_1_Indx82.txt 13,748,578 6,730,117 49.0% 1,924,080.0 354,384.0 114.0 73.0 0.640350877