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Rui:Hap analysis on HL108
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==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 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 ===Stat. of mapping=== {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Indx*.log''' | align="center" style="background:#f0f0f0;"|'''reads processed''' | align="center" style="background:#f0f0f0;"|'''reads w/ at least one reported alignment''' | align="center" style="background:#f0f0f0;"|'''%''' | align="center" style="background:#f0f0f0;"|'''reads failed to align''' | align="center" style="background:#f0f0f0;"|'''%''' | align="center" style="background:#f0f0f0;"|'''reads suppressed due to -m''' | align="center" style="background:#f0f0f0;"|'''%''' | align="center" style="background:#f0f0f0;"|'''unique.bam''' | align="center" style="background:#f0f0f0;"|'''%''' | align="center" style="background:#f0f0f0;"|'''genome coverage''' | align="center" style="background:#f0f0f0;"|'''%''' |- | Indx73_hg18||3,401,036||2,626,988||0.772408172||172,775||0.050800697||601,273||0.176791131||2,287,907||0.672708845||45,686,905||1.5% |- | Indx74_hg18||3,076,200||2,375,127||0.772097718||137,575||0.044722385||563,498||0.183179897||1,816,377||0.590461283||24,773,669||0.8% |- | Indx75_hg18||5,999,843||2,939,753||0.489971654||255,493||0.042583281||2,804,597||0.467445065||266,980||0.044497831||1,029,078 |- | Indx76_hg18||5,045,399||3,968,708||0.786599434||306,293||0.060707389||770,398||0.152693176||293,069||0.058086387||835,201 |- | Indx77_hg18||3,724,017||3,062,199||0.82228384||161,088||0.043256516||500,730||0.134459644||463,450||0.124448949||1,311,157 |- | Indx78_hg18||4,398,109||3,092,220||0.703079437||277,431||0.06307961||1,028,458||0.233840953||281,088||0.063911104||796,051 |- | Indx79_hg18||3,979,607||3,146,004||0.790531326||202,034||0.050767325||631,569||0.158701349||632,079||0.158829503||3,399,419 |- | Indx80_hg18||4,559,310||3,974,449||0.871721598||201,495||0.044194187||383,366||0.084084214||146,583||0.03215026||699,754 |} ===pileup files=== * pileup files to call variation against ref genome nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx73.bowtie.sorted.bam > Indx73.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx74.bowtie.sorted.bam > Indx74.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx75.bowtie.sorted.bam > Indx75.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx76.bowtie.sorted.bam > Indx76.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx77.bowtie.sorted.bam > Indx77.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx78.bowtie.sorted.bam > Indx78.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx79.bowtie.sorted.bam > Indx79.pileup & nohup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m Indx80.bowtie.sorted.bam > Indx80.pileup & 2.14.12 correction: pileup.sh samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx73.bowtie.sorted.bam > Indx73.pileup.2.14.12 samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx74.bowtie.sorted.bam > Indx74.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx75.bowtie.sorted.bam > Indx75.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx76.bowtie.sorted.bam > Indx76.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx77.bowtie.sorted.bam > Indx77.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx78.bowtie.sorted.bam > Indx78.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx79.bowtie.sorted.bam > Indx79.pileup samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/HsB36m.fa Indx80.bowtie.sorted.bam > Indx80.pileup * count unique variations along pileup file wc -l *.pileup 45686905 Indx73.pileup 24773669 Indx74.pileup 1029078 Indx75.pileup 835201 Indx76.pileup 1311157 Indx77.pileup 796051 Indx78.pileup 3399419 Indx79.pileup 699754 Indx80.pileup 78531234 total * histogram for bias analysis vi pileup2his.pl chmod 755 pileup2his.pl ./pileup2his.pl < Indx76.pileup | more ./pileup2his.pl < Indx73.pileup > Indx73_rd_histogram.txt & ./pileup2his.pl < Indx74.pileup > Indx74_rd_histogram.txt & ./pileup2his.pl < Indx75.pileup > Indx75_rd_histogram.txt & ./pileup2his.pl < Indx76.pileup > Indx76_rd_histogram.txt & ./pileup2his.pl < Indx77.pileup > Indx77_rd_histogram.txt & ./pileup2his.pl < Indx78.pileup > Indx78_rd_histogram.txt & ./pileup2his.pl < Indx79.pileup > Indx79_rd_histogram.txt & ./pileup2his.pl < Indx80.pileup > Indx80_rd_histogram.txt & * Comparison of 4 libraries: Indx73, 74, 76 and 80 [[File:11.15.11_bias.jpg]] ===idiographica=== * run script nohup ./pileupVsRefHap.pl Indx73.pileup > Indx73.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx74.pileup > Indx74.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx75.pileup > Indx75.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx76.pileup > Indx76.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx77.pileup > Indx77.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx78.pileup > Indx78.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx79.pileup > Indx79.idioGraph.txt & nohup ./pileupVsRefHap.pl Indx80.pileup > Indx80.idioGraph.txt & * wc -l *.idioGraph.txt 5752 Indx73.idioGraph.txt 2743 Indx74.idioGraph.txt 214 Indx75.idioGraph.txt 86 Indx76.idioGraph.txt 151 Indx77.idioGraph.txt 79 Indx78.idioGraph.txt 365 Indx79.idioGraph.txt 96 Indx80.idioGraph.txt 9486 total * Visualize the parental alleles along Chr. [[File:Indx73.png|600px]][[File:Indx74.png|600px]] [[File:Indx75.png|600px]][[File:Indx76.png|600px]] [[File:Indx77.png|600px]][[File:Indx78.png|600px]] [[File:Indx79.png|600px]][[File:Indx80.png|600px]]
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