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.$asmtesttype.txt''  were generated. Other outputs files were generated as usual. I repeated run ASM again with the N37 sample which have the complete results after ASM run. However, this time I got similar result to the ASM-ASCM data set. I need to figure out what's wrong with the pipeline I used to run ASM. Actually the Master Execution Script was, PipelineExecute-NP.pl, was not edited in other parts except my my ''$root = "/home/expresso/Noi_ASM/20120802.ASM-ASCM/";'' line.
* 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 generate 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.  
* 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 it is available in the right directory.
  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 notice that when the pipeline called ''library(qvalue)'' in R, it showed the below message
  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

[Link to calendar]

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.