Noi/NOTES/2012-7-20
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ASM analysis of the ten tissue of N37 sample[edit]
- ASM analysis of this data set was put on hold due to the fastq file format. The issue are:
- The readIDs format is incompatible to Robert's pipeline
- The quality score of this data set is Phred33 based. It is supposed to be Phred64 to fit to the pieline
- Dr. Zhang helped me to fix these issues (detailed will be added later)
On genome miner: Directory of fastq files: /home/kunzhang/CpgMIP/Data/N37_10_tissues/fastq Directory running ASM: /home/expresso/Noi_ASM/N37_10tissues Sample list (in fastq files) N37-colon.fastq N37-CRBL.fastq N37-FL.fastq N37-heart.fastq N37-liver.fastq N37-lung.fastq N37-pancreas.fastq N37-SI.fastq N37-SM.fastq N37-stomach.fastq Changed one line in PipelineExecute-NP.pl script my $root = "/home/expresso/Noi_ASM/N37_10tissues/"; my $readlength = 74;
Sample IDs | Class I | Class II | Class III | Total | % of class I | % of class II | % of class III |
ASM.N37CRBL.txt | 543 | 217 | 2,175 | 2,935 | 18.50 | 7.39 | 74.11 |
ASM.N37FL.txt | 482 | 265 | 2,808 | 3,555 | 13.56 | 7.45 | 78.99 |
ASM.N37Liver.txt | 343 | 146 | 1,761 | 2,250 | 15.24 | 6.49 | 78.27 |
ASM.N37SI.txt | 599 | 249 | 2,519 | 3,367 | 17.79 | 7.40 | 74.81 |
ASM.N37SM.txt | 527 | 196 | 1,846 | 2,569 | 20.51 | 7.63 | 71.86 |
ASM.N37colon.txt | 500 | 197 | 2,031 | 2,728 | 18.33 | 7.22 | 74.45 |
ASM.N37heart.txt | 322 | 164 | 1,896 | 2,382 | 13.52 | 6.88 | 79.60 |
ASM.N37lung.txt | 732 | 255 | 2,289 | 3,276 | 22.34 | 7.78 | 69.87 |
ASM.N37pancreas.txt | 487 | 201 | 2,118 | 2,806 | 17.36 | 7.16 | 75.48 |
ASM.N37stomach.txt | 543 | 232 | 2,117 | 2,892 | 18.78 | 8.02 | 73.20 |
SNP files | Homozygous SNPs |
Heterozygous SNPS |
Total | % of ASM regions to # of heterozygous SNPs |
SNPs.N37CRBL.txt | 9,781 | 10,159 | 19,940 | 28.89 |
SNPs.N37FL.txt | 11,041 | 11,782 | 22,823 | 30.17 |
SNPs.N37Liver.txt | 8,398 | 8,468 | 16,866 | 26.57 |
SNPs.N37SI.txt | 10,444 | 10,950 | 21,394 | 30.75 |
SNPs.N37SM.txt | 8,816 | 8,973 | 17,789 | 28.63 |
SNPs.N37colon.txt | 8,835 | 8,921 | 17,756 | 30.58 |
SNPs.N37heart.txt | 8,677 | 8,878 | 17,555 | 26.83 |
SNPs.N37lung.txt | 9,928 | 10,101 | 20,029 | 32.43 |
SNPs.N37pancreas.txt | 9,694 | 10,051 | 19,745 | 27.92 |
SNPs.N37stomach.txt | 9,383 | 9,680 | 19,063 | 29.88 |