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''' Link to calendar:'''[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]]<br>
''' Link to calendar:'''[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]]<br>
''' SNP 134 data base :''' on genome-miner: /media/nomeDB/HsGenome/snp134_snv.txt<br>
''' Some oligos info.'''<br>
'''genemapster address: '''genemapster.dynamic.ucsd.edu<br>
* AP2V4: 5’- /Phos/TAGCCTCATGCGTATCCGAT-3’
* DpnII_oligo_v4: 5'-ATGCGTATCCGATC-3'
* AP2V6: 5’-/5Phos/CACGGGTAGTGTGTATCCTG-3’
* RE-DpnII-V6: 5’-GTGTATCCTGATC-3’
 
'''Install R packages:''' install.packages("package_name")<br>
''' SNP 134 data base :''' on genome-miner: /media/Ext4T/GenomeDB/HsGenome/snp134_snv.txt<br>
'''genemapster address: '''nplongth@genemapster.dynamic.ucsd.edu<br>
'''meangenemachine address:''' nplongth@132.239.189.236<br>
<br>
'''General unix commands'''
print the last field of each line
awk '{ print $NF }' file > output
print a certain field to the last field
awk '{substr($0, index($0,$3))}'
this command to print out column #3 to the last field ($0=the whole line)
substitute specific field
awk -F'delimiter' -vOFS='delimiter' '{sub("to_be_replaced", "replaced_with", field_to_be_replaced); print}'
Example: to replace : sign in column1 with tab
awk -F'\t' -vOFS='\t' '{ gsub(":", "\t", $1); print }'
awk command to do matching or searching of string or word "ONLY"
/\<WORD-TO-SEARCH-HERE\>/
 
'''Triton'''
* New triton account '''ssh nplongth@tscc-login.sdsc.edu''' (May 2013)
Also change job file: #PBS -A k4zhang-group
To submit job file: qsub -q home-k4zhang job_name
* '''checkjob -v jobid''' = job diagnosis
* '''gbalance -p zhang-lab''' = check credit balance of zhang-lab
'''Unix'''
* Kill job by user ID
ps -U USER_ID
kill PID
 
'''R plotting'''
* Set margin on bottom, left, top, and right of the plot
op <- par(mar=c(6, 6, 4, 2) + 0.1) the number could be optimized
* Multiple plots on the same axis
plot(x, y1, ylim=range(c(y1,y2)))
par(new=TRUE)
plot(x, y2, ylim=range(c(y1,y2)), axes = FALSE, xlab = "", ylab = "")
* Example of histogram plot, set log scale on Y-axis --> the plot does'n look really nice. Using gap.plot is much better and the scale look more real.
A=read.table("10%FDR_allCpG-SNP-2MB_mQTL_CpG-SNP_distance2",sep="\t")
head(A)
B=abs(A$V4)/1000
h <- hist(B, breaks=2000, plot=FALSE)
pdf("SNP-CpG_distance_all_CpG.mQTL_log.pdf",height=7.5, width=10)
plot(h$mids, h$counts, log="y", type='h',main="all CpG mQTL", col="#104E8B",lwd=4, ylab="Frequency", xlab="Distance between SNPs and CpG sites (kb)", cex.lab=1.5)
axis(side = 1, at = seq(0,2000,250))
'''http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm'''<br>
'''http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm'''<br>
'''R:Data structure:''' http://www.statmethods.net/input/datatypes.html<br>
'''R: Graphic parameters, text & symbol size, plotting symbols, lines, colors, fonts, margins and graph size:'''http://www.statmethods.net/advgraphs/parameters.html<br>
'''R: color chart:'''http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf<br>
'''Multiple testing correction:'''[[Media:MultipleTestCorrection_Agilent.pdf| MultipleTestCorrection_Agilent]]
'''Multiple testing correction:'''[[Media:MultipleTestCorrection_Agilent.pdf| MultipleTestCorrection_Agilent]]
* Note to read: (2012-04_19)
** http://bioinformatics.oxfordjournals.org/content/20/12/1896.long
** http://cdn.intechopen.com/pdfs/22507/InTech-Algorithms_for_cpg_islands_search_new_advantages_and_old_problems.pdf
** http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002629
** http://www.genetics.org/content/early/2012/01/23/genetics.111.137737.full.pdf
* Read: (2012_04_23)
** PCA analysis: http://strata.uga.edu/software/pdf/pcaTutorial.pdf
** PCA script example: http://stat.ethz.ch/~maathuis/teaching/fall08/Rscript-PCA.R
** Suggestion from Dr. Zhang: http://www.pnas.org/content/early/2012/04/18/1201310109.full.pdf+html
* 2012_04_25
** QDA and LDA function in matlab: http://www.mathworks.com/products/statistics/demos.html?file=/products/demos/shipping/stats/classdemo.html
** Good LDA tutorial: https://onlinecourses.science.psu.edu/stat857/book/export/html/17
* 2012_04_27
** Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution (New report from Sciencexpress): http://www.sciencemag.org/content/early/2012/04/25/science.1220671.full.pdf
* 2012_06_07
** PreCR Repair Mix: http://www.neb.com/nebecomm/products/productM0309.asp
** Dr. Zhang used to mention about designing "well-controlled experiment to test whether pre-treatment with this PreCR Repair Mix can improve either BSPP or tagmentation/PCR?"
'''Dinh:COMPUTATIONAL/bisReadMapper''': http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh:COMPUTATIONAL/bisReadMapper<br>
'''BEDtools and Table browser (to get annotated file)'''
* http://code.google.com/p/bedtools/
* http://genome.ucsc.edu/cgi-bin/hgTables?org=Human&db=hg19&hgsid=280495487&hgta_doMainPage=1
Group: Genes and Gene Prediction Tracks
Track: RefSeq Genes
Table: RefGenes
* Dr. Zhang suggest to try '''EZ-96 DNA Methylation-Gold™ MagPrep''' (2012/06/28) : http://www.zymoresearch.com/downloads/dl/file/id/494/d5042i.pdf
* Human imprinted genes: http://www.geneimprint.com/site/genes-by-species.Homo+sapiens.any
* Binding buffer for AmPure bead purification: P4137 - PEG / NaCl Solution. 500ml (Teknova)
** 20% PEG 800
** 2.5M NaCl
* http://www.1000genomes.org/sites/1000genomes.org/files/docs/PilotsSummary.pdf
* http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-197/samples.html
* Check chromosome and coordinate of CpG and SNP derived from mapping by bisReadMapperSE19Triton and from Robert's ASM pipeline: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-27]]
* wget with user name ans password: wget --user=USERNAMEXX --password='PASSWORDXX' http://www.XXX
* Alternative polymerase for padlock extension: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2008-5-14]]

Latest revision as of 22:23, 26 June 2013

Link to calendar:[[1]]
Some oligos info.

  • AP2V4: 5’- /Phos/TAGCCTCATGCGTATCCGAT-3’
  • DpnII_oligo_v4: 5'-ATGCGTATCCGATC-3'
  • AP2V6: 5’-/5Phos/CACGGGTAGTGTGTATCCTG-3’
  • RE-DpnII-V6: 5’-GTGTATCCTGATC-3’

Install R packages: install.packages("package_name")
SNP 134 data base : on genome-miner: /media/Ext4T/GenomeDB/HsGenome/snp134_snv.txt
genemapster address: nplongth@genemapster.dynamic.ucsd.edu
meangenemachine address: nplongth@132.239.189.236

General unix commands
print the last field of each line
awk '{ print $NF }' file > output

print a certain field to the last field
awk '{substr($0, index($0,$3))}'
this command to print out column #3 to the last field ($0=the whole line)

substitute specific field
awk -F'delimiter' -vOFS='delimiter' '{sub("to_be_replaced", "replaced_with", field_to_be_replaced); print}'
Example: to replace : sign in column1 with tab
awk -F'\t' -vOFS='\t' '{ gsub(":", "\t", $1); print }'

awk command to do matching or searching of string or word "ONLY" 
/\<WORD-TO-SEARCH-HERE\>/

Triton

  • New triton account ssh nplongth@tscc-login.sdsc.edu (May 2013)
Also change job file: #PBS -A k4zhang-group
To submit job file: qsub -q home-k4zhang job_name
  • checkjob -v jobid = job diagnosis
  • gbalance -p zhang-lab = check credit balance of zhang-lab

Unix

  • Kill job by user ID
ps -U USER_ID
kill PID

R plotting

  • Set margin on bottom, left, top, and right of the plot
op <- par(mar=c(6, 6, 4, 2) + 0.1) the number could be optimized
  • Multiple plots on the same axis
plot(x, y1, ylim=range(c(y1,y2)))
par(new=TRUE)
plot(x, y2, ylim=range(c(y1,y2)), axes = FALSE, xlab = "", ylab = "")
  • Example of histogram plot, set log scale on Y-axis --> the plot does'n look really nice. Using gap.plot is much better and the scale look more real.
A=read.table("10%FDR_allCpG-SNP-2MB_mQTL_CpG-SNP_distance2",sep="\t")
head(A)
B=abs(A$V4)/1000
h <- hist(B, breaks=2000, plot=FALSE)
pdf("SNP-CpG_distance_all_CpG.mQTL_log.pdf",height=7.5, width=10)
plot(h$mids, h$counts, log="y", type='h',main="all CpG mQTL", col="#104E8B",lwd=4, ylab="Frequency", xlab="Distance between SNPs and CpG sites (kb)", cex.lab=1.5)
axis(side = 1, at = seq(0,2000,250))

http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
R:Data structure: http://www.statmethods.net/input/datatypes.html
R: Graphic parameters, text & symbol size, plotting symbols, lines, colors, fonts, margins and graph size:http://www.statmethods.net/advgraphs/parameters.html
R: color chart:http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf
Multiple testing correction: MultipleTestCorrection_Agilent

Dinh:COMPUTATIONAL/bisReadMapper: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh:COMPUTATIONAL/bisReadMapper
BEDtools and Table browser (to get annotated file)

Group: Genes and Gene Prediction Tracks
Track: RefSeq Genes
Table: RefGenes