Rui:Hap analysis on HL108: Difference between revisions
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| align="center" style="background:#f0f0f0;"|'''%''' | | align="center" style="background:#f0f0f0;"|'''%''' | ||
| align="center" style="background:#f0f0f0;"|'''genome coverage''' | | 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 | | 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 | | 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 | | 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 |
Latest revision as of 00:14, 10 March 2012
Hap analysis on HL101 (repeat on 3.9.12)[edit]
HL101 | processed reads | reads w/ at least one reported alignment | % | reads failed to align | % | reads suppressed due to -m | % | unique.bam | % | genome coverage | % |
Rui_Indx10 | 7,553,726 | 4,839,648 | 0.64 | 1,882,671 | 0.25 | 831,407 | 0.11 | 2,049,951 | 0.27 | 118,904,934 | 4% |
Rui_Indx12 | 2,323,928 | 1,517,533 | 0.65 | 538,277 | 0.23 | 268,118 | 0.12 | 723,044 | 0.31 | 42,555,438 | 1.5% |
Hap analysis on HL108 11.14.11[edit]
- 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[edit]
- 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[edit]
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[edit]
Indx*.log | reads processed | reads w/ at least one reported alignment | % | reads failed to align | % | reads suppressed due to -m | % | unique.bam | % | genome coverage | % |
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[edit]
- 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
idiographica[edit]
- 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.pngFile:Indx74.png File:Indx75.pngFile:Indx76.png File:Indx77.pngFile:Indx78.png File:Indx79.pngFile:Indx80.png