Rui:Hap analysis on HL108: Difference between revisions
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>RuiLiu m (→rmdup) |
>RuiLiu m (→rmdup) |
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/home/kunzhang/softwares/samtools-0.1.12a/samtools view -c -q 250 Indx73.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;"|'''%''' | |||
|- | |||
| 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 | |||
|} |
Revision as of 18:49, 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 |