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>
= 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.$asmtesttype.txt''  were generated. Other outputs files were generated as usual. I repeated run ASM again with the N37 sample which have the complete results after ASM run. However, this time I got similar result to the ASM-ASCM data set. I need to figure out what's wrong with the pipeline I used to run ASM. Actually the Master Execution Script was, PipelineExecute-NP.pl, was not edited in other parts except my my ''$root = "/home/expresso/Noi_ASM/20120802.ASM-ASCM/";'' line.

Revision as of 21:23, 6 August 2012

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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 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, $expname.log.txt of N37 sample and ASM-ASCM samples.
** In N37colon.log.txt file
/home/expresso/Noi_ASM/N37_10tissues//N37colon: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/N37_10tissues/ N37colon /home/expresso//mysqlcredentials.txt /home/expresso//hg19/refFlat.txt (2012-7-19 at 23:47:48).
CHR: 1!
CHR: N!
Missed: 515 Found: 2213! 
CHR: 1!
CHR: N!
** In DF2ASCM.log.txt file
/home/expresso/Noi_ASM/20120802.ASM-ASCM//DF2ASCM: perl /home/expresso//STARASMAnnotate.pl /home/expresso/Noi_ASM/20120802.ASM-ASCM/ DF2ASCM /home/expresso//mysqlcredenti
als.txt /home/expresso//hg19/refFlat.txt (2012-8-2 at 16:18:34).
Missed: 0 Found: 0!
It's possible that there is something wrong when it ran STARASMAnnotate.pl script. I also checked the availability of refFlat.txt file it it is available in the right directory.
* I need to figure out whats wrong with the STARASMAnnotate.pl run
For MFASMAnalysisQValues.$expname.$asmtesttype.txt file generation. I notice that when the pipeline called library(qvalue) in R, it showed the below message 
> library(qvalue);
Error in library(qvalue) : there is no package called ‘qvalue’
Execution halted
This is different from the previous run that the  MFASMAnalysisQValues.$expname.$asmtesttype.txt files were successfully generated
> library(qvalue);
Loading Tcl/Tk interface ... done
Warning message:
In fun(...) : no DISPLAY variable so Tk is not available
I expect that the qvalue library was removed.
I then re-installed qvalue library 
 
Save and uncompressed qvalue_1.1.tar.gz 
Install: R CMD INSTALL qvalue_1.1.tar (as root)

Then I reran the ASM again on P10E3ASCM sample