Rui:RNAseq analysis on 121226 HL140

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Revision as of 00:13, 3 January 2013 by >RuiLiu (→‎Reads information)
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RNAseq on 121226_HL140

  • Continue with Kun's note [1]
  • A number of questions that I hope to answer with this data set include:
  1. Is there any indication that we can obtain reasonable data from 10pg of input total RNA?
  2. Is there a difference in efficiency between TSOs with and without the 8bp barcodes?
  3. Is there a difference in efficiency between T20V and T20VN primer?
  4. Is there a difference in efficiency between 72C and 10C annealing?
  5. Is NTC clean enough compared with 10pg samples?

Reads information

  • Reads number for each T20 libraries was based on the counts of lines in each fastq file
  • However, the total reads from sum of T20.id01 to T20.id16 were not consistent with the ones from the log file [2]?
Input ng # N2.id01_avg N2.id02_avg N2.id03_avg N2.id04_avg
0 2 0.18% 0.16% 0.81% 0.54%
0.1 12 2.58% 2.63% 3.60% 3.48%
1 2 34.36% 34.07% 27.62% 28.60%
total Reads 3,146,372 2,366,588 4,194,796 3,431,696
Input ng # N2.id05_avg N2.id06_avg N2.id07_avg N2.id08_avg
0 2 0.70% 0.84% 3.47% 3.53%
0.01 12 2.76% 2.81% 5.26% 5.24%
0.1 2 32.73% 32.32% 14.95% 15.03%
total reads 3,483,059 1,668,975 5,572,495 1,774,114