Rui:RNAseq analysis on 121226 HL140: Difference between revisions
Jump to navigation
Jump to search
>RuiLiu |
>RuiLiu |
||
Line 12: | Line 12: | ||
* 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:
- Is there any indication that we can obtain reasonable data from 10pg of input total RNA?
- Is there a difference in efficiency between TSOs with and without the 8bp barcodes?
- Is there a difference in efficiency between T20V and T20VN primer?
- Is there a difference in efficiency between 72C and 10C annealing?
- 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 |