software:topical:lifescience:qa

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software:topical:lifescience:qa [2019/10/24 15:51]
meesters [Meta Assessment Tools]
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-====== Quality Assessment of NGS Data ====== 
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-Checking the quality((Quality checks or assessments are different to quality control or enhancement.)) of experimental data is crucial to data analysis. 
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-===== Software Options ===== 
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-==== Individual Assessment Tools ==== 
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-=== FastQC === 
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-One of the best-known tools for estimating the sequencing quality (and providing summary statistics and plots) is [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]]. 
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-We provide this software as [[:setting_up_environment_modules|modules]] under: 
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-''bio/FastQC'' 
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-You can find a wrapper to ease your workflow, [[software:topical:lifescience:qa#the_wrapper_module_on_mogon|below]]. 
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-<WRAP center round info 90%> 
-You can visualize the html-files created by FastQC with ''firefox'', which is installed on both clusters. 
-</WRAP> 
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-==== Meta Assessment Tools ==== 
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-[[https://deeptools.readthedocs.io/|deepTools]] grant a number of assesment tools. It is available as the module file(s): 
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-''bio/deepTools'' 
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-[[https://multiqc.info/|MultiQC]] is an assessment tool to gather the output of multiple quality indicators and to visualize them. 
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-It is available as a module file: 
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-''bio/MultiQC'' 
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-Both might be run in job context or outside. 
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-===== The Wrapper Module on Mogon ===== 
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-We provide a wrapper module on Mogon in order to aggregate jobs and to integrate the quality check into a workflow. 
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-The wrapper script is available as a [[:setting_up_environment_modules|module]]: 
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-''bio/parallel_QATools'' 
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-The code is under version management and hosted internally, [[https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis|here]]. 
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-<WRAP center round important 90%> 
-The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one. 
-</WRAP> 
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-Calling ''QAWrapper -h'' will display a help message with all the options, the script provides. Likewise, the call ''QAWrapper --credits'' will display credits and a version history. 
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-The script, after loading the module, can then be run like: 
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-<code bash> 
-$ QAWrapper --executable=<executable> [options] <inputdir> 
-</code> 
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-<WRAP center round info 90%> 
-**Different meanings of the selected executable** 
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-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. 
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-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> 
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-About Arguments: 
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-  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:qa|quality assessment module]]. 
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-The options: 
-  * ''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. 
-  * ''-p,--partition'', the default is ''nodeshort'' or ''parallel'' on Mogon2, no smp-partition should be choosen. 
-  * ''--args'', arguments otherwise not set by the wrapper - the defaults of the choosen executable apply for unset arguments 
-  * ''-d,--dependency'', list of comma separated jobids, the job will wait for to finish 
-  * ''-o,--outdir'',  output directory path (default is the current working directory) 
-  * ''--constraint'', on Mogon II, only: defaults to ''broadwell'' 
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-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''| 
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-Output: 
-  * One analysis per input as specified by the respective executable. 
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