Rui:Hap analysis on HL108: Difference between revisions
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>RuiLiu m (→fastq2bam.pl) |
>RuiLiu m (→rmdup) |
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nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx80.bowtie.sorted.bam Indx80.bowtie.unique.bam & | nohup /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 view -c Indx73.bowtie.unique.bam | /home/kunzhang/softwares/samtools-0.1.12a/samtools view -c -q 250 Indx73.bowtie.unique.bam |
Revision as of 02:38, 15 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&
rmdup
nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx73.bowtie.sorted.bam Indx73.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx74.bowtie.sorted.bam Indx74.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx75.bowtie.sorted.bam Indx75.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx76.bowtie.sorted.bam Indx76.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx77.bowtie.sorted.bam Indx77.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx78.bowtie.sorted.bam Indx78.bowtie.unique.bam & nohup /home/kunzhang/softwares/samtools-0.1.12a/samtools rmdup -s Indx79.bowtie.sorted.bam Indx79.bowtie.unique.bam & nohup /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 view -c -q 250 Indx73.bowtie.unique.bam