Noi:Quicklinks: Difference between revisions
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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/ | ''' Some oligos info.'''<br> | ||
'''genemapster address: '''genemapster.dynamic.ucsd.edu | * AP2V4: 5’- /Phos/TAGCCTCATGCGTATCCGAT-3’ | ||
'''http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm''' | * 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> | |||
'''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-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
- 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
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: [[2]]
- wget with user name ans password: wget --user=USERNAMEXX --password='PASSWORDXX' http://www.XXX
- Alternative polymerase for padlock extension: [[3]]