EricChu:LabNotesMDA/2015-1-7: Difference between revisions

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* These 9 single cell libraries were sequenced in HL175. GM stands for GM20431.
* 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.
# GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
# PGP1 Dev7 Oct6 (Index 17-24). 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 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 Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
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* ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
* ../../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
* /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
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''bam_file'''
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''Raw_Reads'''
| align="center" style="background:#f0f0f0;"|'''MappingRate'''
| align="center" style="background:#f0f0f0;"|'''MappableReads'''
| align="center" style="background:#f0f0f0;"|'''ClonalRate'''
| align="center" style="background:#f0f0f0;"|'''Unique'''
| align="center" style="background:#f0f0f0;"|''' 1+'''
| align="center" style="background:#f0f0f0;"|''' 1'''
| align="center" style="background:#f0f0f0;"|''' 2'''
| align="center" style="background:#f0f0f0;"|''' 3'''
| align="center" style="background:#f0f0f0;"|''' 4+'''
| align="center" style="background:#f0f0f0;"|'''contig'''
| align="center" style="background:#f0f0f0;"|'''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||
|-
|
|}

Revision as of 00:11, 16 January 2015

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

  1. PGP1 Dev8 Oct6
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