EricChu:LabNotesMDA/2015-1-7

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Revision as of 00:15, 16 January 2015 by >Ericchu
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Mapping New Sequencing Libraries

  • These 9 single cell libraries were sequenced in HL175. GM stands for GM20431.
  1. GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
  2. PGP1 Dev8 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1.
  3. 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.
  4. GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
  5. GM Dev9 Nov14 (Index9-32). Asked for 40 million reads. Sequenced in Lane4.
  6. GM Dev9 Nov18 (Index9-32). Asked for 40 million reads. Sequenced in Lane5.
  7. GM Dev9 Dec2 (Index9-32). Asked for 40 million reads. Sequenced in Lane6.
  8. GM Dev9 Dec3 (Index9-32). Asked for 40 million reads. Sequenced in Lane7.
  9. 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