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''' Link to calendar:'''[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]]<br> ''' Some oligos info.'''<br> * AP2V4: 5β- /Phos/TAGCCTCATGCGTATCCGAT-3β * DpnII_oligo_v4: 5'-ATGCGTATCCGATC-3' * AP2V6: 5β-/5Phos/CACGGGTAGTGTGTATCCTG-3β * RE-DpnII-V6: 5β-GTGTATCCTGATC-3β '''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> '''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]] * 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-Goldβ’ 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]]
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