Noi/NOTES/2012-8-6: Difference between revisions
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[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']]<br> | [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']]<br> | ||
= ASM analysis on ASM-ASCM data set problems = | = ASM analysis on ASM-ASCM data set problems = | ||
* I have performed and finished ASM run on ASM-ASCM data set. I found every sample doesn't contain ''ASM.$expname.bed'', ''ASM.$expname.txt'', and ''ASMref.$expname.txt'' data in the output files and also no ''MFASMAnalysisQValues.$expname.$asmtesttype.txt'' were generated. Other outputs files were generated as usual. I repeated run ASM again with the N37 sample which have the complete results after ASM run. However, this time I got similar result to the ASM-ASCM data set. I need to figure out what's wrong with the pipeline I used to run ASM. Actually the Master Execution Script | * I have performed and finished ASM run on ASM-ASCM data set. I found every sample doesn't contain ''ASM.$expname.bed'', ''ASM.$expname.txt'', and ''ASMref.$expname.txt'' data in the output files and also no ''MFASMAnalysisQValues.$expname.$asmtesttype.txt'' were generated. Other outputs files were generated as usual. I repeated run ASM again with the N37 sample which have the complete results after ASM run. However, this time I got similar result to the ASM-ASCM data set. I need to figure out what's wrong with the pipeline I used to run ASM. Actually the Master Execution Script, PipelineExecute-NP.pl, was not edited in other parts except ''my $root = "/home/expresso/Noi_ASM/20120802.ASM-ASCM/";'' line. | ||
* I then checked the script that | * I then checked the script that used to classify the ASM class, and I guess it should be ''STARASMAnnotate.pl''. I looked up and compare the log file for the pipeline, $expname.log.txt of N37 sample and ASM-ASCM samples. | ||
** In N37colon.log.txt file | ** In N37colon.log.txt file | ||
/home/expresso/Noi_ASM/N37_10tissues//N37colon: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/N37_10tissues/ N37colon /home/expresso//mysqlcredentials.txt /home/expresso//hg19/refFlat.txt (2012-7-19 at 23:47:48). | /home/expresso/Noi_ASM/N37_10tissues//N37colon: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/N37_10tissues/ N37colon /home/expresso//mysqlcredentials.txt /home/expresso//hg19/refFlat.txt (2012-7-19 at 23:47:48). | ||
Line 14: | Line 14: | ||
als.txt /home/expresso//hg19/refFlat.txt (2012-8-2 at 16:18:34). | als.txt /home/expresso//hg19/refFlat.txt (2012-8-2 at 16:18:34). | ||
Missed: 0 Found: 0! | Missed: 0 Found: 0! | ||
It's possible that there is something wrong when it ran STARASMAnnotate.pl script. I also checked the availability of refFlat.txt file | It's possible that there is something wrong when it ran STARASMAnnotate.pl script. I also checked the availability of refFlat.txt file. It exists in the right directory. | ||
* I need to figure out whats wrong with the STARASMAnnotate.pl run | * I need to figure out whats wrong with the STARASMAnnotate.pl run | ||
For ''MFASMAnalysisQValues.$expname.$asmtesttype.txt'' file generation. I | For ''MFASMAnalysisQValues.$expname.$asmtesttype.txt'' file generation. I noticed that when the pipeline called ''library(qvalue)'' in R, it showed below messages | ||
> library(qvalue); | > library(qvalue); | ||
Error in library(qvalue) : there is no package called ‘qvalue’ | Error in library(qvalue) : there is no package called ‘qvalue’ | ||
Line 27: | Line 27: | ||
In fun(...) : no DISPLAY variable so Tk is not available | In fun(...) : no DISPLAY variable so Tk is not available | ||
I think that the qvalue library was removed. | I think that the qvalue library was removed. (searching online: Package ‘qvalue’ was removed from the CRAN repository) | ||
I then re-installed qvalue library | I then re-installed qvalue library | ||
Revision as of 04:17, 7 August 2012
ASM analysis on ASM-ASCM data set problems
- I have performed and finished ASM run on ASM-ASCM data set. I found every sample doesn't contain ASM.$expname.bed, ASM.$expname.txt, and ASMref.$expname.txt data in the output files and also no MFASMAnalysisQValues.$expname.$asmtesttype.txt were generated. Other outputs files were generated as usual. I repeated run ASM again with the N37 sample which have the complete results after ASM run. However, this time I got similar result to the ASM-ASCM data set. I need to figure out what's wrong with the pipeline I used to run ASM. Actually the Master Execution Script, PipelineExecute-NP.pl, was not edited in other parts except my $root = "/home/expresso/Noi_ASM/20120802.ASM-ASCM/"; line.
- I then checked the script that used to classify the ASM class, and I guess it should be STARASMAnnotate.pl. I looked up and compare the log file for the pipeline, $expname.log.txt of N37 sample and ASM-ASCM samples.
** In N37colon.log.txt file /home/expresso/Noi_ASM/N37_10tissues//N37colon: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/N37_10tissues/ N37colon /home/expresso//mysqlcredentials.txt /home/expresso//hg19/refFlat.txt (2012-7-19 at 23:47:48). CHR: 1! CHR: N! Missed: 515 Found: 2213! CHR: 1! CHR: N! ** In DF2ASCM.log.txt file /home/expresso/Noi_ASM/20120802.ASM-ASCM//DF2ASCM: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/20120802.ASM-ASCM/ DF2ASCM /home/expresso//mysqlcredenti als.txt /home/expresso//hg19/refFlat.txt (2012-8-2 at 16:18:34). Missed: 0 Found: 0! It's possible that there is something wrong when it ran STARASMAnnotate.pl script. I also checked the availability of refFlat.txt file. It exists in the right directory. * I need to figure out whats wrong with the STARASMAnnotate.pl run
For MFASMAnalysisQValues.$expname.$asmtesttype.txt file generation. I noticed that when the pipeline called library(qvalue) in R, it showed below messages > library(qvalue); Error in library(qvalue) : there is no package called ‘qvalue’ Execution halted This is different from the previous run that the MFASMAnalysisQValues.$expname.$asmtesttype.txt files were successfully generated > library(qvalue); Loading Tcl/Tk interface ... done Warning messages: In fun(...) : no DISPLAY variable so Tk is not available I think that the qvalue library was removed. (searching online: Package ‘qvalue’ was removed from the CRAN repository) I then re-installed qvalue library In /home/expresso directory: Save and uncompressed: qvalue_1.1.tar.gz file Install: R CMD INSTALL qvalue_1.1.tar (as root) # Then I re-ran the ASM again on P10E3ASCM sample # Quick look after I ran ASM on P10E3ASCM sample for a while. The log file show number of Missed and Found after running, /home/expresso/Noi_ASM/20120802.ASM-ASCM//P10E3ASCM: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/20120802.ASM-ASCM/ P10E3ASCM /home/expresso//mysqlcredentials.txt /home/expresso//hg19/refFlat.txt (2012-8-6 at 14:48:44). CHR: 1! CHR: N! Missed: 165 Found: 788! CHR: 1! CHR: N! And also MFASMAnalysisQValues.$expname.$asmtesttype.txt files were generated after I install qvalue library. I still have no idea how qvalue library get involve in STARASMAnnotate.pl. I will take a deep look into details in that script. # Once the ASM run done, I got all output files I want for ASM analysis. Then I start to repeat analysis on other samples.