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