Kun:LabNotes/GenomeSeq/2013-6-15
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Data analysis of the third PGP1 cells[edit]
- Hosuk did the amplification and amplicon extraction. He used a slower mixing and lower KOH concentration to avoid excessive DNA damage.
- Noi constructed the libraries.
- Sequencing was performed in HL154, 50% of Lane 4 and 100% of Lane 7, SE36+7 reads.
Library | Raw_reads | Mapping_rate | Mappable_reads | Clonal_rate | 1+ | 1 | 2 | 3 | 4+ |
HL154-HSL-PGP1-June4_Indx09 | 3,046,875 | 98.44% | 2,999,294 | 0.8577 | 5,055,775 | 3,250,676 | 606,810 | 250,611 | 935,050 |
HL154-HSL-PGP1-June4_Indx10 | 2,839,916 | 95.24% | 2,704,758 | 0.8424 | 4,066,194 | 2,600,783 | 421,754 | 169,135 | 857,959 |
HL154-HSL-PGP1-June4_Indx11 | 3,160,303 | 98.96% | 3,127,378 | 0.9025 | 3,112,645 | 2,088,295 | 323,568 | 129,161 | 555,136 |
HL154-HSL-PGP1-June4_Indx12 | 2,650,212 | 98.57% | 2,612,346 | 0.9134 | 2,534,151 | 1,765,505 | 280,636 | 105,155 | 373,716 |
HL154-HSL-PGP1-June4_Indx13 | 3,018,682 | 98.61% | 2,976,825 | 0.908 | 2,828,285 | 1,916,281 | 284,036 | 118,674 | 497,474 |
HL154-HSL-PGP1-June4_Indx14 | 3,320,365 | 98.78% | 3,279,773 | 0.9016 | 3,303,635 | 2,263,756 | 343,186 | 132,414 | 547,775 |
HL154-HSL-PGP1-June4_Indx15 | 1,777,529 | 98.22% | 1,745,834 | 0.6706 | 5,842,769 | 3,578,417 | 729,552 | 288,223 | 1,230,259 |
HL154-HSL-PGP1-June4_Indx16 | 2,905,699 | 98.74% | 2,869,141 | 0.6874 | 7,567,818 | 4,610,238 | 757,727 | 301,298 | 1,882,006 |
HL154-HSL-PGP1-June4_Indx17 | 2,569,434 | 98.42% | 2,528,836 | 0.7446 | 5,323,875 | 3,241,562 | 501,135 | 208,936 | 1,355,721 |
HL154-HSL-PGP1-June4_Indx18 | 2,603,016 | 98.12% | 2,554,130 | 0.6966 | 6,907,672 | 3,992,513 | 769,671 | 343,762 | 1,785,178 |
HL154-HSL-PGP1-June4_Indx19 | 2,508,037 | 98.21% | 2,463,034 | 0.7099 | 7,050,967 | 4,311,747 | 824,038 | 332,709 | 1,565,919 |
HL154-HSL-PGP1-June4_Indx20 | 2,036,668 | 97.86% | 1,993,023 | 0.6545 | 5,955,475 | 3,418,117 | 602,918 | 269,067 | 1,648,823 |
HL154-HSL-PGP1-June4_Indx21 | 2,687,448 | 98.64% | 2,650,790 | 0.6586 | 7,532,080 | 4,416,498 | 746,925 | 321,270 | 2,030,841 |
HL154-HSL-PGP1-June4_Indx22 | 2,844,075 | 98.47% | 2,800,692 | 0.6698 | 8,652,159 | 5,314,014 | 940,876 | 380,946 | 1,999,763 |
HL154-HSL-PGP1-June4_Indx23 | 3,161,089 | 96.92% | 3,063,663 | 0.6949 | 8,040,240 | 4,449,145 | 867,736 | 401,182 | 2,305,614 |
HL154-HSL-PGP1-June4_Indx24 | 2,883,798 | 98.34% | 2,836,002 | 0.7137 | 7,059,052 | 4,142,979 | 713,605 | 313,832 | 1,873,118 |
HL154-HSL-PGP1-June4_Indx25 | 1,906,394 | 97.70% | 1,862,477 | 0.6118 | 6,560,072 | 3,759,050 | 675,301 | 314,092 | 1,795,346 |
HL154-HSL-PGP1-June4_Indx26 | 1,874,894 | 98.58% | 1,848,223 | 0.6762 | 5,590,507 | 3,391,894 | 576,177 | 251,583 | 1,354,308 |
HL154-HSL-PGP1-June4_Indx27 | 1,906,657 | 98.80% | 1,883,855 | 0.6614 | 5,381,553 | 3,186,537 | 522,240 | 229,564 | 1,426,705 |
HL154-HSL-PGP1-June4_Indx28 | 1,801,285 | 98.24% | 1,769,633 | 0.6468 | 5,229,116 | 2,977,559 | 511,038 | 244,178 | 1,479,782 |
HL154-HSL-PGP1-June4_Indx29 | 2,265,674 | 97.27% | 2,203,766 | 0.6576 | 6,666,084 | 3,859,133 | 684,057 | 303,194 | 1,803,181 |
HL154-HSL-PGP1-June4_Indx30 | 2,129,636 | 97.90% | 2,084,867 | 0.6877 | 6,038,899 | 3,609,352 | 609,496 | 266,324 | 1,537,167 |
HL154-HSL-PGP1-June4_Indx31 | 3,148,226 | 98.63% | 3,105,124 | 0.8398 | 6,722,352 | 4,346,394 | 897,073 | 364,993 | 1,097,451 |
HL154-HSL-PGP1-June4_Indx32 | 2,817,025 | 97.72% | 2,752,791 | 0.8499 | 4,749,410 | 2,941,390 | 533,315 | 245,338 | 1,016,043 |
File:HL154-HSL-PGP1-chr19.png
- There are several issue with this batch of data:
- First, based on the SeqMonk coverage plot, DNA amplification is extremely sparse, and the cross-talk among different reactors is stronger. The latter could be also due to the read mapping.
- Second, there isn't clear evidence of big DNA molecules separated into individual reactors.
- Third, the clonal rate is much higher, which is probably also due to the poor amplification.
- Overall, there is something wrong with this experiment, either due to slow/incomplete mixing, or low KOH concentration. The next experiment needs to be design carefully to distinguish these two.