EricChu:LabNotesMDA/2015-1-7
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Mapping New Sequencing Libraries
- These 9 single cell libraries were sequenced in HL175. GM stands for GM20431.
- GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
- PGP1 Dev8 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1.
- GM Dev9.2 Oct23 (Index 25-32). Asked for 20 million reads. Sequenced in Lane 1. GM Dev9.2 Oct23 (Index 9-24). Asked for 40 million reads. Sequenced in Lane 2.
- GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
- GM Dev9 Nov14 (Index9-32). Asked for 40 million reads. Sequenced in Lane4.
- GM Dev9 Nov18 (Index9-32). Asked for 40 million reads. Sequenced in Lane5.
- GM Dev9 Dec2 (Index9-32). Asked for 40 million reads. Sequenced in Lane6.
- GM Dev9 Dec3 (Index9-32). Asked for 40 million reads. Sequenced in Lane7.
- GM Dev7 Dec9 (Index9-32). Asked for 40 million reads. Sequenced in Lane8.
Commands
- reference: http://genome-tech.ucsd.edu/LabNotes/index.php/EricChu:LabNotesMDA/2014-8-25
- txt files were copied to /data_Syn_15T/HL175/
- Each single cell data have its own folder.
- For example, in /data_Syn_15T/HL175/GMDev9Oct10
- command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log &
- ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
- /home/kunzhang/softwares/samtools-0.1.19/samtools view -o s_1_1_Indx32_unique.sam s_1_1_Indx32_unique.bam
Summaries of Sequencing Results
PGP1 Dev8 Oct6: 400mM ALS 8min pump, NS 0min
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | Mito % |
s_1_1_Indx17_sorted.bam | 9 | 217,653 | 81.27% | 176,890 | 2.58% | 172,326 | 7,047,215 | 5,906,698 | 808,250 | 193,693 | 123,844 | 50 | 0.72% |
s_1_1_Indx18_sorted.bam | 10 | 371,006 | 82.14% | 304,742 | 2.77% | 296,301 | 11,816,162 | 9,631,704 | 1,525,191 | 390,584 | 254,448 | 113 | 0.35% |
s_1_1_Indx19_sorted.bam | 11 | 230,506 | 82.31% | 189,741 | 2.49% | 185,016 | 7,609,472 | 6,384,424 | 869,077 | 208,944 | 133,657 | 41 | 0.45% |
s_1_1_Indx20_sorted.bam | 12 | 220,926 | 82.00% | 181,160 | 2.89% | 175,924 | 6,900,560 | 5,585,808 | 889,076 | 239,564 | 171,647 | 77 | 0.64% |
s_1_1_Indx21_sorted.bam | 13 | 241,578 | 82.45% | 199,187 | 2.67% | 193,869 | 7,686,007 | 6,217,752 | 1,019,302 | 270,080 | 164,393 | 80 | 0.64% |
s_1_1_Indx22_sorted.bam | 14 | 290,676 | 83.34% | 242,246 | 3.18% | 234,543 | 8,994,661 | 7,116,771 | 1,254,370 | 357,017 | 250,797 | 123 | 0.81% |
s_1_1_Indx23_sorted.bam | 15 | 358,363 | 82.65% | 296,176 | 3.67% | 285,306 | 10,525,718 | 8,192,296 | 1,461,782 | 457,003 | 398,991 | 172 | 0.65% |
s_1_1_Indx24_sorted.bam | 16 | 423,102 | 84.62% | 358,023 | 4.23% | 342,879 | 11,668,130 | 8,449,278 | 1,926,598 | 656,706 | 619,634 | 282 | 0.65% |
2,353,810 | 1,948,165 | 1,886,164 | 938 | ||||||||||
GM Dev9 Oct10: 400mM ALS 5min pump, NS 2min
bam_file | sample | Raw_Reads | MappingRate | MappableReads | ClonalRate | Unique | 1+ | 1 | 2 | 3 | 4+ | contig | mito % |
s_1_1_Indx09_sorted.bam | 1 | 1,185,461 | 92.15% | 1,092,352 | 9.88% | 984,428 | 25566539 | 16430816 | 4066655 | 1834422 | 3218141 | 776 | 0.65% |
s_1_1_Indx10_sorted.bam | 2 | 878,051 | 92.41% | 811,404 | 4.22% | 777,163 | 28763373 | 22943333 | 3614129 | 1068962 | 1120592 | 416 | 0.35% |
s_1_1_Indx11_sorted.bam | 3 | 599,446 | 92.85% | 556,598 | 3.51% | 537,061 | 20323989 | 16273884 | 2530109 | 786467 | 717353 | 332 | 0.37% |
s_1_1_Indx12_sorted.bam | 4 | 964,470 | 92.25% | 889,682 | 10.86% | 793,063 | 20340153 | 13258220 | 3172788 | 1393513 | 2499128 | 641 | 0.87% |
s_1_1_Indx13_sorted.bam | 5 | 1,080,380 | 92.43% | 998,608 | 7.60% | 922,714 | 28568106 | 20506465 | 4219661 | 1610385 | 2215033 | 771 | 1.21% |
s_1_1_Indx14_sorted.bam | 6 | 1,371,077 | 91.62% | 1,256,193 | 15.20% | 1,065,252 | 22584672 | 13334265 | 3538903 | 1720474 | 3974593 | 821 | 0.27% |
s_1_1_Indx15_sorted.bam | 7 | 588,560 | 91.64% | 539,373 | 6.66% | 503,451 | 15656188 | 11296394 | 2257865 | 866065 | 1219354 | 420 | 0.82% |
s_1_1_Indx16_sorted.bam | 8 | 1,545,679 | 91.87% | 1,419,958 | 18.28% | 1,160,390 | 18788455 | 8802440 | 3049596 | 1746533 | 5173393 | 828 | 0.43% |
8,213,124 | 7,564,168 | 6,743,520 | 5005 | ||||||||||