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 | # 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.
- 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
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 | ||||||||||