Noi/NOTES/2012-7-20: Difference between revisions
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my $root = "/home/expresso/Noi_ASM/N37_10tissues/"; | my $root = "/home/expresso/Noi_ASM/N37_10tissues/"; | ||
my $readlength = 74; | my $readlength = 74; | ||
{| {{table}} border = 1 | |||
| width="160pt" align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| width="70pt" align="center" style="background:#f0f0f0;"|'''Class I''' | |||
| width="70pt" align="center" style="background:#f0f0f0;"|'''Class II''' | |||
| width="70pt" align="center" style="background:#f0f0f0;"|'''Class III''' | |||
| width="80pt" align="center" style="background:#f0f0f0;"|'''Total''' | |||
| align="center" style="background:#f0f0f0;"|'''% of class I''' | |||
| align="center" style="background:#f0f0f0;"|'''% of class II''' | |||
| align="center" style="background:#f0f0f0;"|'''% 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 | |||
|} | |||
{| {{table}} border = 1 | |||
| width="160pt" align="center" style="background:#f0f0f0;"|'''SNP files''' | |||
| align="center" style="background:#f0f0f0;"|'''Homozygous<br> SNPs''' | |||
| align="center" style="background:#f0f0f0;"|'''Heterozygous<br> SNPS''' | |||
| width="80pt" align="center" style="background:#f0f0f0;"|'''Total''' | |||
| align="center" style="background:#f0f0f0;"|'''% of ASM regions to <br># 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 | |||
|} |
Latest revision as of 21:36, 6 August 2012
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 |