Kun:LabNotes/Haplotyping/2011-11-12

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Analysis of HL108 lane7-8 data[edit]

  • Rui made the libraries from (how many cells) of (what is the cell line), by limited MDA on diluted cell lysates followed by tagmentation (what is the wiki page).
  • The pooled library was sequenced in two lanes (s7 & s8). I pooled the data from the two lanes based on the barcodes.
  • I did the mapping using the script /home/kunzhang/bin/fastq2bamHg19.pl (should have used fastq2bam.pl because Idiographica doesn't support hg19).
nohup fastq2bamHg19.pl Indx74.txt > Indx74.log&
nohup fastq2bamHg19.pl Indx75.txt > Indx75.log&
nohup fastq2bamHg19.pl Indx76.txt > Indx76.log&
nohup fastq2bamHg19.pl Indx77.txt > Indx77.log&
nohup fastq2bamHg19.pl Indx78.txt > Indx78.log&
nohup fastq2bamHg19.pl Indx79.txt > Indx79.log&
nohup fastq2bamHg19.pl Indx80.txt > Indx80.log&
  • I then generated pileup files:
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx74.bowtie.sorted.bam > Indx74.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx75.bowtie.sorted.bam > Indx75.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx76.bowtie.sorted.bam > Indx76.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx77.bowtie.sorted.bam > Indx77.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx78.bowtie.sorted.bam > Indx78.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx79.bowtie.sorted.bam > Indx79.pileup &
 /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx80.bowtie.sorted.bam > Indx80.pileup &
  • Commands for removing clonal reads and counting reads in bam files:
/home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx80.bowtie.sorted.bam Indx80.bowtie.unique.bam &
/home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx79.bowtie.sorted.bam Indx79.bowtie.unique.bam &
/home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx78.bowtie.sorted.bam Indx78.bowtie.unique.bam &
/home/kunzhang/softwares/samtools-0.1.12a/samtools view -c Indx79.bowtie.unique.bam 
/home/kunzhang/softwares/samtools-0.1.12a/samtools view -c Indx79.bowtie.sorted.bam