Noi/NOTES/2012-7-20: Difference between revisions

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>Noi
(Created page with "http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar'''<br> = ASM analysis of the ten tissue of N37 sample = * ASM analysis of this data...")
 
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  N37-SM.fastq
  N37-SM.fastq
  N37-stomach.fastq
  N37-stomach.fastq
Changed one line in PipelineExecute-NP.pl script
my $root = "/home/expresso/Noi_ASM/N37_10tissues/";
my $readlength = 74;

Revision as of 01:07, 20 July 2012

[Link to calendar]

ASM analysis of the ten tissue of N37 sample

  • 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;