Rui:Hap analysis on HL108
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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&