Rui:Hap analysis on HL108: Difference between revisions

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>RuiLiu
>RuiLiu
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| Indx80_hg18||4,559,310||3,974,449||0.871721598||201,495||0.044194187||383,366||0.084084214||146,583||0.03215026
| Indx80_hg18||4,559,310||3,974,449||0.871721598||201,495||0.044194187||383,366||0.084084214||146,583||0.03215026
|}
|}
===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 &

Revision as of 19:41, 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

Stat. of mapping

Indx*.log reads processed reads w/ at least one reported alignment % reads failed to align % reads suppressed due to -m % unique.bam %
Indx73_hg18 3,401,036 2,626,988 0.772408172 172,775 0.050800697 601,273 0.176791131 2,287,907 0.672708845
Indx74_hg18 3,076,200 2,375,127 0.772097718 137,575 0.044722385 563,498 0.183179897 1,816,377 0.590461283
Indx75_hg18 5,999,843 2,939,753 0.489971654 255,493 0.042583281 2,804,597 0.467445065 266,980 0.044497831
Indx76_hg18 5,045,399 3,968,708 0.786599434 306,293 0.060707389 770,398 0.152693176 293,069 0.058086387
Indx77_hg18 3,724,017 3,062,199 0.82228384 161,088 0.043256516 500,730 0.134459644 463,450 0.124448949
Indx78_hg18 4,398,109 3,092,220 0.703079437 277,431 0.06307961 1,028,458 0.233840953 281,088 0.063911104
Indx79_hg18 3,979,607 3,146,004 0.790531326 202,034 0.050767325 631,569 0.158701349 632,079 0.158829503
Indx80_hg18 4,559,310 3,974,449 0.871721598 201,495 0.044194187 383,366 0.084084214 146,583 0.03215026

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 &