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Rui:RNAseq analysis on 121226 HL140
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==RNAseq on 121226_HL140== * Library prep. [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/SingleCell/2012-12-17] * Continue with Kun's note [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2013-1-1] * 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 * Double check the log file [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2013-1-1] to see if it is consistent with the table 1. It seems #1,3,5,7 are better than #2,4,6,8. But, it may also due to stringency of decoding BC8. {| {{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||3,752,306||89.51% |- | N2_id02||3,539,471||3,161,228||89.31% |- | N2_id03||5,579,440||4,951,860||88.75% |- | N2_id04||5,649,610||5,053,225||89.44% |- | N2_id05||4,926,765||4,314,228||87.57% |- | N2_id06||2,879,929||2,416,335||83.90% |- | N2_id07||7,703,629||6,637,310||86.16% |- | N2_id08||3,696,754||3,148,127||85.16% |} * Generally, N2.id07 and N2.id08 do not follow others regarding to relative fractions for each category and comparison between T20VN and T20V, mainly due to wired counts on T20.id13 to T20.id16 (T20V primers) {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Input ng''' | align="center" style="background:#f0f0f0;"|'''#''' | align="center" style="background:#f0f0f0;"|'''N2.id01_avg''' | align="center" style="background:#f0f0f0;"|'''N2.id02_avg''' | align="center" style="background:#f0f0f0;"|'''N2.id03_avg''' | align="center" style="background:#f0f0f0;"|'''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 |} {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Input ng''' | align="center" style="background:#f0f0f0;"|'''#''' | align="center" style="background:#f0f0f0;"|'''N2.id05_avg''' | align="center" style="background:#f0f0f0;"|'''N2.id06_avg''' | align="center" style="background:#f0f0f0;"|'''N2.id07_avg''' | align="center" style="background:#f0f0f0;"|'''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 |}
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