Revision as of 01:25, 12 March 2012 by >RuiLiu
Data
- Library: RL_Fib100c_29s_ExoCap_Jan31.2012; RL_EF_ExoCap_Jan31.2012 [1]
- fq: genome-miner:/media/SeqStore2/120211_HL114/RL_Exome (s2 and s3)
- Analysis: genome-miner:~/Ext12T/HL114
Mapping
- Instruction: [2]
- Script: fastq2fixedBam.pl (rmdup off; SNP call off)
- Upload file: HL114.unix.info <for fastq2fixedBam.pl>; HL114_Athurva.unix.info <for latest version of variantCallerBwaGATK.pl>
tr "\r" "\n" < HL114.info > HL114.unix.info
tr "\r" "\n" < HL114_Athurva.info > HL114_Athurva.unix.info
nohup ./fastq2fixedBam.pl HL114.unix.info &> HL114.unix.status &
- Output: HL114.fixed.bam
- De-multiplexing: split_bam_file.pl
- Output: HL114_index.fixed.bam
Genome coverage
- Script: bam_to_pileup.pl
- Input: HL114_index.fixed.bam
- Output: HL114_index.pileup; HL114_(index).exom_cov_stat.txt
Amplification bias
- Script: getBlockCoverage.pl
- Input: HL114_index.pileup
- Output: HL114_Indx.bedGraph.txt
SNP calling
- Script: mPileup2sncTable.pl
- Input: HL114_all index.pileup
- Output: MM_libraries_snc_matrix_1.txt (>=1) MM_libraries_snc_matrix_2.txt (>=2)
Analysis
Basic stat
- Take the two extremes as the example for analysis
HL114
|
Raw Reads
|
Mapped Reads
|
Mapping rate
|
'
|
Genomic Coverage (1x)
|
Genomic Coverage (8x)
|
Genomic Coverage (20x)
|
'
|
Exomic Coverage (1x)
|
Exomic Coverage (8x)
|
Exomic Coverage (20x)
|
ExoCap (1x)
|
ExoCap (8x)
|
ExoCap (20x)
|
%target_covered (1X)
|
%target_covered (8X)
|
%target_covered (20X)
|
Indx84 |
3,466,058 |
3,006,065 |
0.86728641 |
|
115,157,379 |
4,957,071 |
1,497,440 |
|
8,601,392 |
1,967,268 |
816,346 |
0.074692495 |
0.396860969 |
0.545161075 |
0.194945125 |
0.044586888 |
0.018501967
|
Indx80 |
1,164,032 |
954,899 |
0.820337413 |
|
51,214,017 |
1,279,455 |
309,971 |
|
5,429,531 |
625,099 |
168,536 |
0.106016503 |
0.488566616 |
0.54371538 |
0.123056896 |
0.014167475 |
0.003819762
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Indx90 |
2,758,235 |
2,379,233 |
0.862592564 |
|
87,506,864 |
3,746,156 |
1,288,719 |
|
4,935,581 |
1,621,741 |
770,420 |
0.056402215 |
0.432908026 |
0.597818454 |
0.111861831 |
0.036755737 |
0.017461083
|
Indx92 |
454,131 |
384,678 |
0.847063953 |
|
10,043,141 |
741,152 |
249,113 |
|
722,367 |
211,249 |
119,838 |
0.071926402 |
0.285027903 |
0.481058797 |
0.016371992 |
0.004787825 |
0.002716053
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Indx7 |
2,651,616 |
2,301,606 |
0.868001249 |
|
52,315,891 |
4,812,671 |
1,377,887 |
|
2,273,297 |
1,020,041 |
613,853 |
0.043453279 |
0.21194904 |
0.445503151 |
0.051522843 |
0.023118586 |
0.013912591
|
Indx8 |
621,535 |
281,492 |
0.452898067 |
|
7,429,177 |
606,175 |
187,171 |
|
547,137 |
115,081 |
52,532 |
0.073647054 |
0.189847816 |
0.280663137 |
0.012400515 |
0.002608238 |
0.001190605
|
- Comparison with HL100 (made by Alice, 5000cells (F), 2000c (E), 1000c (D) are made by Tn-PCR and Agilent ExoCap
HL100
|
Raw Reads
|
Mapped Reads
|
Mapping rate
|
'
|
Genomic Coverage (1x)
|
Genomic Coverage (5x)
|
Genomic Coverage (10x)
|
'
|
Exomic Coverage (1x)
|
Exomic Coverage (5x)
|
Exomic Coverage (10x)
|
ExoCap (1x)
|
ExoCap (5x)
|
ExoCap (10x)
|
ExomeF |
14,859,867 |
11,805,582 |
0.794460812 |
|
410,572,508 |
3,674,020 |
747,354 |
|
19,568,285 |
935,295 |
39,821 |
0.047660972 |
0.254569926 |
0.053282648
|
ExomeE |
10,979,686 |
8,627,530 |
0.785772016 |
|
346,235,444 |
3,609,706 |
643,995 |
|
19,895,849 |
1,080,242 |
44,391 |
0.057463351 |
0.299260383 |
0.068930659
|
ExomeD |
3,781,861 |
3,158,964 |
0.835293523 |
|
157,788,154 |
1,330,861 |
237,732 |
|
15,098,670 |
338,691 |
15,338 |
0.095689503 |
0.254490138 |
0.064518029
|