Rui:Hap analysis on HL108

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Revision as of 19:26, 14 November 2011 by >RuiLiu (Created page with '==Hap analysis on HL108 11.14.11== * Dr. Zhang's notes on 11.12.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-11-12] * Dr. Zhang's message on 1…')
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Hap analysis on HL108 11.14.11

  • Dr. Zhang's notes on 11.12.11 [1]
  • Dr. Zhang's message on 11.12.11: Some numbers we would like to see include: # raw reads, # mappable reads, # clonal reads, total bps covered. We also need to look at the distribution of read depth using histograms.
  • Each library needs a unique ID in a well-define format that can be found both in the sequencing log and the wiki page describing the experiment.

fastq2bam.pl

  • copy seq files under own directory, otherwise the writing permission will be denied.
ln -s /home/kunzhang/haplotyping/Data/HL108 ~/HL108_seq
cp ~/HL108_seq/*.txt ./

  • test fastq2bam.pl scrip (hg18)
mkdir Indx74
cd Indx74
nohup /home/kunzhang/bin/fastq2bam.pl ../Indx74.txt > Indx74.log&