Rui:RNAseq analysis on 121226 HL140: Difference between revisions

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* However, the total reads from sum of T20.id01 to T20.id16 were not consistent with the ones from the log file [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2013-1-1]?
* However, the total reads from sum of T20.id01 to T20.id16 were not consistent with the ones from the log file [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2013-1-1]?
* Generally, N2.id07 and N2.id08 do not follow others, mainly due to wired counts on T20.id13 to T20.id16 (T20V primers)
* Generally, N2.id07 and N2.id08 do not follow others, mainly due to wired counts on T20.id13 to T20.id16 (T20V primers)
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''N2_index'''
| align="center" style="background:#f0f0f0;"|'''total'''
| align="center" style="background:#f0f0f0;"|'''decoded'''
| align="center" style="background:#f0f0f0;"|'''%'''
|-
| N2_id01||4,191,926||3,146,372||75.06%
|-
| N2_id02||3,539,471||2,366,588||66.86%
|-
| N2_id03||5,579,440||4,194,796||75.18%
|-
| N2_id04||5,649,610||3,431,696||60.74%
|-
| N2_id05||4,926,765||3,483,059||70.70%
|-
| N2_id06||2,879,929||1,668,975||57.95%
|-
| N2_id07||7,703,629||5,572,495||72.34%
|-
| N2_id08||3,696,754||1,774,114||47.99%
|}


{| {{table}} border=1
{| {{table}} border=1

Revision as of 19:28, 3 January 2013

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]?
  • Generally, N2.id07 and N2.id08 do not follow others, mainly due to wired counts on T20.id13 to T20.id16 (T20V primers)
N2_index total decoded %
N2_id01 4,191,926 3,146,372 75.06%
N2_id02 3,539,471 2,366,588 66.86%
N2_id03 5,579,440 4,194,796 75.18%
N2_id04 5,649,610 3,431,696 60.74%
N2_id05 4,926,765 3,483,059 70.70%
N2_id06 2,879,929 1,668,975 57.95%
N2_id07 7,703,629 5,572,495 72.34%
N2_id08 3,696,754 1,774,114 47.99%
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