Rui:Hap analysis on HL108: Difference between revisions

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Line 8: Line 8:
  ln -s /home/kunzhang/haplotyping/Data/HL108 ~/HL108_seq
  ln -s /home/kunzhang/haplotyping/Data/HL108 ~/HL108_seq
  cp ~/HL108_seq/*.txt ./
  cp ~/HL108_seq/*.txt ./
* Need to transfer files (esp. seq files) to external disc, otherwise it will overload into root
ln -s ln -s /media/Ext4T/DataDrive.backup/RL_Scratch/Hap/HL108 ./Hap
   
   
* test fastq2bam.pl scrip (hg18) - seting up a folder is unnecessary  
* test fastq2bam.pl scrip (hg18) - seting up a folder is unnecessary  
nohup /home/kunzhang/bin/fastq2bam.pl Indx73.txt > Indx73.log&
  nohup /home/kunzhang/bin/fastq2bam.pl Indx74.txt > Indx74.log&
  nohup /home/kunzhang/bin/fastq2bam.pl Indx74.txt > Indx74.log&
  nohup /home/kunzhang/bin/fastq2bam.pl Indx75.txt > Indx75.log&
  nohup /home/kunzhang/bin/fastq2bam.pl Indx75.txt > Indx75.log&

Revision as of 23:06, 14 November 2011

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 ./
  • Need to transfer files (esp. seq files) to external disc, otherwise it will overload into root
ln -s ln -s /media/Ext4T/DataDrive.backup/RL_Scratch/Hap/HL108 ./Hap

  • test fastq2bam.pl scrip (hg18) - seting up a folder is unnecessary
nohup /home/kunzhang/bin/fastq2bam.pl Indx73.txt > Indx73.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx74.txt > Indx74.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx75.txt > Indx75.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx76.txt > Indx76.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx77.txt > Indx77.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx78.txt > Indx78.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx79.txt > Indx79.log&
nohup /home/kunzhang/bin/fastq2bam.pl Indx80.txt > Indx80.log&