software:topical:lifescience:qa

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software:topical:lifescience:qa [2019/03/12 09:02]
meesters
software:topical:lifescience:qa [2019/10/24 15:51]
meesters [Meta Assessment Tools]
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 ==== Meta Assessment Tools ==== ==== Meta Assessment Tools ====
 +
 +[[https://​deeptools.readthedocs.io/​|deepTools]] grant a number of assesment tools. It is available as the module file(s):
 +
 +''​bio/​deepTools''​
  
 [[https://​multiqc.info/​|MultiQC]] is an assessment tool to gather the output of multiple quality indicators and to visualize them. [[https://​multiqc.info/​|MultiQC]] is an assessment tool to gather the output of multiple quality indicators and to visualize them.
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 ''​bio/​MultiQC''​ ''​bio/​MultiQC''​
  
-It can be run in job to complete a pipeline with a quality assessment.+Both might be run in job context or outside.
  
 ===== The Wrapper Module on Mogon ===== ===== The Wrapper Module on Mogon =====
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 <WRAP center round info 90%> <WRAP center round info 90%>
-The current release only supports FastQC. Therefore, the ''​--executable''​ is meaningless.+**Different meanings of the selected executable** 
 + 
 +Obviously''​fastqc''​ is to determine ​the quality of the "​raw"​ data in FASTQ format. Yet, other executables are available, such as ''​samtools'' ​with their invocation on ''​.bam''​ file to summarize the quality of mapping tools. 
 + 
 +See below for a detailed description. If a particular executable ​is not supported, [[https://​gitlab.rlp.net/​hpc-jgu-lifescience/​seq-analysis/​issues|you can approach us]].
 </​WRAP>​ </​WRAP>​
  
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 The options: The options:
   * ''​QAWrapper''​ attempts to deduce your SLURM account. This may fail, in which case ''​-A,​ --account''​ needs to be supplied.   * ''​QAWrapper''​ attempts to deduce your SLURM account. This may fail, in which case ''​-A,​ --account''​ needs to be supplied.
 +  * ''​--executable'',​ defaults to ''​fastqc''​. Other options: ''​samtools''​. Option is case-insensitive.
   * ''​-l,​--runlimit'',​ this defaults to 300 minutes.   * ''​-l,​--runlimit'',​ this defaults to 300 minutes.
   * ''​-p,​--partition'',​ the default is ''​nodeshort''​ or ''​parallel''​ on Mogon2, no smp-partition should be choosen.   * ''​-p,​--partition'',​ the default is ''​nodeshort''​ or ''​parallel''​ on Mogon2, no smp-partition should be choosen.
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   * ''​-o,​--outdir'', ​ output directory path (default is the current working directory)   * ''​-o,​--outdir'', ​ output directory path (default is the current working directory)
   * ''​--constraint'',​ on Mogon II, only: defaults to ''​broadwell''​   * ''​--constraint'',​ on Mogon II, only: defaults to ''​broadwell''​
 +
 +Executables:​
 +^ Selected ​    ^ Recognized Files       ^ Purpose ​         ^  Invocation ^
 +| ''​fastqc'' ​  | FASTQ files ending on ''​.fastq'',​ ''​.fq''​ or ''​.gz''​ | assess quality of raw or trimmed data | |
 +| ''​samtools''​ | mapped ''​.bam''​ files | assess quality of mapped (sorted or filtered) compressed data| ''​samtools flagstat''​|
  
 Output: Output:
  • software/topical/lifescience/qa.txt
  • Last modified: 2019/10/24 15:51
  • by meesters