Lower mapping rates of TX2094 20dpa
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huguanjing commented
Compare to others, TX2094 20dpa samples were mapped at a lower rate. Fastqc showed that these libraries have higher sequence duplication levels, indicating some kind of enrichment bias in generating their RNA-seq libraries, or RNA extraction difficulty with this sampling condition. Below is bowtie2 mapping results, what about bwa?
| FileName | ID | Sample | Accession | DPA | Replicate | Total read pairs | Mapped read pairs, before filter | Percentage mapped, before filter | Filtered read pairs | Mapped read pairs, after filter | Percentage mapped, after filter |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1F1-10dpa-fiber_211_L4 | SRR___ | MxT.10dpa.1 | MxT | 10 | 1 | 10,756,588 | 6,550,540 | 60.90% | 8,339,787 | 5,289,268 | 63.42% |
| 1F1-20dpa-fiber_205_L6 | SRR | MxT.20dpa.1 | MxT | 20 | 1 | 8,985,380 | 6,081,245 | 67.68% | 7,273,294 | 5,032,400 | 69.19% |
| 2F1-10dpa-fiber_211_L6 | SRR | MxT.10dpa.2 | MxT | 10 | 2 | 10,110,567 | 5,991,744 | 59.26% | 7,736,080 | 4,791,512 | 61.94% |
| 2F1-20dpa-fiber_206_L6 | SRR | MxT.20dpa.2 | MxT | 20 | 2 | 11,494,379 | 6,892,959 | 59.97% | 9,053,072 | 5,645,434 | 62.36% |
| 3F1-10dpa-fiber_212_L6 | SRR | MxT.10dpa.3 | MxT | 10 | 3 | 10,740,520 | 6,040,743 | 56.24% | 8,415,058 | 4,929,312 | 58.58% |
| 3F1-20dpa-fiber_207_L6 | SRR | MxT.20dpa.3 | MxT | 20 | 3 | 10,778,185 | 6,720,667 | 62.35% | 8,505,719 | 5,493,802 | 64.59% |
| 4F1-10dpa-fiber_222_L3 | SRR | TxM.10dpa.1 | TxM | 10 | 1 | 10,026,565 | 5,957,055 | 59.41% | 7,743,695 | 4,778,911 | 61.71% |
| 4F1-20dpa-fiber_208_L6 | SRR | TxM.20dpa.1 | TxM | 20 | 1 | 9,685,175 | 5,902,473 | 60.94% | 7,555,762 | 4,799,165 | 63.52% |
| 5F1-10dpa-fiber_223_L3 | SRR | TxM.10dpa.2 | TxM | 10 | 2 | 10,000,290 | 5,754,267 | 57.54% | 7,742,836 | 4,637,623 | 59.90% |
| 5F1-20dpa-fiber_209_L6 | SRR | TxM.20dpa.2 | TxM | 20 | 2 | 10,178,768 | 6,161,627 | 60.53% | 7,848,956 | 4,969,025 | 63.31% |
| 6F1-10dpa-fiber_225_L3 | SRR | TxM.10dpa.3 | TxM | 10 | 3 | 10,815,961 | 6,497,172 | 60.07% | 8,561,927 | 5,320,525 | 62.14% |
| 6F1-20dpa-fiber_210_L6 | SRR | TxM.20dpa.3 | TxM | 20 | 3 | 10,780,275 | 6,493,999 | 60.24% | 8,485,359 | 5,324,456 | 62.75% |
| maxxa-09-10dpa-fiber_204_L4 | SRR | maxxa.10dpa.1 | maxxa | 10 | 1 | 9,839,562 | 5,472,538 | 55.62% | 7,748,114 | 4,527,265 | 58.43% |
| maxxa-09-20dpa-fiber_227_L3 | SRR | maxxa.20dpa.1 | maxxa | 20 | 1 | 9,986,304 | 5,706,169 | 57.14% | 7,731,307 | 4,611,609 | 59.65% |
| maxxa-110-10dpa-fiber_206_L4 | SRR | maxxa.10dpa.2 | maxxa | 10 | 2 | 11,374,202 | 5,948,914 | 52.30% | 8,855,933 | 4,880,761 | 55.11% |
| maxxa-110-20dpa-fiber_202_L4 | SRR | maxxa.20dpa.2 | maxxa | 20 | 2 | 10,779,389 | 5,954,233 | 55.24% | 8,332,873 | 4,840,624 | 58.09% |
| maxxa-112-10dpa-fiber_205_L4 | SRR | maxxa.10dpa.3 | maxxa | 10 | 3 | 10,593,243 | 5,822,964 | 54.97% | 8,191,443 | 4,755,849 | 58.06% |
| maxxa-112-20dpa-fiber_201_L4 | SRR | maxxa.20dpa.3 | maxxa | 20 | 3 | 10,045,980 | 6,324,495 | 62.96% | 7,778,110 | 5,064,390 | 65.11% |
| maxxa-113-10dpa-fiber_212_L4 | SRR | maxxa.10dpa.4 | maxxa | 10 | 4 | 10,773,224 | 6,184,122 | 57.40% | 8,498,186 | 5,094,055 | 59.94% |
| maxxa-113-20dpa-fiber_203_L4 | SRR | maxxa.20dpa.4 | maxxa | 20 | 4 | 9,646,587 | 5,363,382 | 55.60% | 7,402,978 | 4,326,106 | 58.44% |
| TX2094-1-10dpa-fiber_207_L4 | SRR | TX2094.10dpa.1 | TX2094 | 10 | 1 | 11,309,911 | 6,275,701 | 55.49% | 8,769,774 | 5,127,955 | 58.47% |
| TX2094-1-20dpa-fiber_222_L4 | SRR | TX2094.20dpa.1 | TX2094 | 20 | 1 | 10,770,070 | 4,305,532 | 39.98% | 8,202,094 | 3,481,409 | 42.45% |
| TX2094-2-10dpa-fiber_208_L4 | SRR | TX2094.10dpa.2 | TX2094 | 10 | 2 | 9,971,759 | 6,076,658 | 60.94% | 7,937,583 | 5,031,944 | 63.39% |
| TX2094-2-20dpa-fiber_223_L4 | SRR | TX2094.20dpa.2 | TX2094 | 20 | 2 | 11,483,824 | 3,899,080 | 33.95% | 8,736,588 | 3,151,079 | 36.07% |
| TX2094-3-10dpa-fiber_201 | SRR | TX2094.10dpa.3 | TX2094 | 10 | 3 | 11,206,757 | 5,683,089 | 50.71% | 8,079,067 | 4,485,017 | 55.51% |
| TX2094-3-20dpa-fiber_225_L4 | SRR | TX2094.20dpa.3 | TX2094 | 20 | 3 | 10,740,479 | 4,112,028 | 38.29% | 8,294,287 | 3,356,538 | 40.47% |
iamcorrinne commented
Let me check when legion gets back online.....