Qualimap
From BITS wiki
Perform various Quality Control checks on BAM data obtained by NGS
: RSeQC
Qualimap [1] is a script toolbox written in python that performs a number of quality control operations as well as data transformation that can prove very useful for RNASeq data analysis (Download from: http://qualimap.bioinfo.cipf.es[2]).
A manual is accessible through the help menu of the Java GUI.
 |
|
|---|---|
 |
 |
Help on command line versions
The command-line version currently groups 3 tools listed below.
- qualimap: When only 'qualimap' is typed, the GUI will start
help for qualimap CLI
qualimap -h Java memory size is set to 1200M Launching application... QualiMap v.0.8 Built on 2014-03-05 17:17 usage: qualimap <tool> [options] To launch GUI leave <tool> empty. Available tools: bamqc Evaluates NGS mapping to a reference genome counts Counts data analysis (RNA-seq data evaluation) clustering Clustering epigenomic signals comp-counts Compute feature counts Special arguments: --java-mem-size Use this argument to set Java memory heap size. Example: qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
- bamqc: Evaluates NGS mapping to a reference genome
help for bamqc
qualimap bamqc -h Java memory size is set to 1200M Launching application... QualiMap v.0.8 Built on 2014-03-05 17:17 Selected tool: bamqc ERROR: Unrecognized option: -h usage: qualimap bamqc -bam <arg> [-c] [-gd <arg>] [-gff <arg>] [-hm <arg>] [-nr <arg>] [-nt <arg>] [-nw <arg>] [-os] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>] [-p <arg>] [-rscriptpath <arg>] -bam <arg> input mapping file -c,--paint-chromosome-limits paint chromosome limits inside charts -gd <arg> compare with genome distribution (possible values: HUMAN or MOUSE) -gff <arg> region file (in GFF/GTF or BED format) -hm <arg> minimum size for a homopolymer to be considered in indel analysis (default is 3) -nr <arg> number of reads in the chunk -nt <arg> number of threads (default is 4) -nw <arg> number of windows (default is 400) -os,--outside-stats compute region outside stats (works only with -gff option) -outdir <arg> output folder -outfile <arg> output file for PDF report (default value is report.pdf) -outformat <arg> output report format (PDF or HTML, default is HTML) -p <arg> specify protocol to calculate correct strand reads (works only with -gff option, possible values are STRAND-SPECIFIC-FORWARD or STRAND-SPECIFIC-REVERSE, default is NON-STRAND-SPECIFIC) -rscriptpath <arg> path to Rscript executable (by default it is assumed to be available from system $PATH) Special arguments: --java-mem-size Use this argument to set Java memory heap size. Example: qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
- counts: Counts data analysis (RNA-seq data evaluation)
help for counts
qualimap counts -h Java memory size is set to 1200M Launching application... QualiMap v.0.8 Built on 2014-03-05 17:17 Selected tool: counts ERROR: Unrecognized option: -h usage: qualimap counts -d1 <arg> [-d2 <arg>] [-i <arg>] [-k <arg>] [-n1 <arg>] [-n2 <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>] [-rscriptpath <arg>] [-s <arg>] -d1,--data1 <arg> first file with counts -d2,--data2 <arg> second file with counts -i,--info <arg> info file -k,--threshold <arg> threshold for the number of counts -n1,--name1 <arg> name for the first sample -n2,--name2 <arg> name for second sample -outdir <arg> output folder -outfile <arg> output file for PDF report (default value is report.pdf) -outformat <arg> output report format (PDF or HTML, default is HTML) -rscriptpath <arg> path to Rscript executable (by default it is assumed to be available from system $PATH) -s,--species <arg> use default file for the given species [human | mouse] Special arguments: --java-mem-size Use this argument to set Java memory heap size. Example: qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
}} * '''clustering''': Clustering epigenomic signals {{Collapsed|margin=20px|comment=help for clustering|content= <syntaxhighlight lang="bash"> qualimap clustering -h Java memory size is set to 1200M Launching application... QualiMap v.0.8 Built on 2014-03-05 17:17 Selected tool: clustering ERROR: Unrecognized option: -h usage: qualimap clustering [-b <arg>] [-c <arg>] -control <arg> [-expr <arg>] [-f <arg>] [-l <arg>] [-name <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>] [-r <arg>] -regions <arg> [-rscriptpath <arg>] -sample <arg> [-viz <arg>] -b,--bin-size <arg> size of the bin (default is 100) -c,--clusters <arg> comma-separated list of cluster sizes -control <arg> comma-separated list of control BAM files -expr <arg> name of the experiment -f,--fragment-length <arg> smoothing length of a fragment -l <arg> upstream offset (default is 2000) -name <arg> comma-separated names of the replicates -outdir <arg> output folder -outfile <arg> output file for PDF report (default value is report.pdf) -outformat <arg> output report format (PDF or HTML, default is HTML) -r <arg> downstream offset (default is 500) -regions <arg> path to regions file -rscriptpath <arg> path to Rscript executable (by default it is assumed to be available from system $PATH) -sample <arg> comma-separated list of sample BAM files -viz <arg> visualization type: heatmap or line Special arguments: --java-mem-size Use this argument to set Java memory heap size. Example: qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
- comp-counts: Compute feature counts
help for comp-counts
qualimap comp-counts -h Java memory size is set to 1200M Launching application... QualiMap v.0.8 Built on 2014-03-05 17:17 Selected tool: comp-counts ERROR: Unrecognized option: -h usage: qualimap comp-counts [-algorithm <arg>] [-b] -bam <arg> -gtf <arg> [-id <arg>] [-out <arg>] [-protocol <arg>] [-rscriptpath <arg>] [-type <arg>] -algorithm <arg> uniquely-mapped-reads(default) or proportional -b GTF-specific. Calculate 5' and 3' coverage bias. -bam <arg> Mapping file in BAM format -gtf <arg> Region file in GTF, GFF or BED format. If GTF format is provided, counting is based on attributes, otherwise based on feature name -id <arg> GTF-specific. Attribute of the GTF to be used as feature ID. Regions with the same ID will be aggregated as part of the same feature. Default: gene_id. -out <arg> Path to output file -protocol <arg> strand-specific-forward,strand-specific-reverse or non-strand-specific -rscriptpath <arg> path to Rscript executable (by default it is assumed to be available from system $PATH) -type <arg> GTF-specific. Value of the third column of the GTF considered for counting. Other types will be ignored. Default: exon Special arguments: --java-mem-size Use this argument to set Java memory heap size. Example: qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
References:
- ↑
Fernando García-Alcalde, Konstantin Okonechnikov, José Carbonell, Luis M Cruz, Stefan Götz, Sonia Tarazona, Joaquín Dopazo, Thomas F Meyer, Ana Conesa
Qualimap: evaluating next-generation sequencing alignment data.
Bioinformatics: 2012, 28(20);2678-9
[PubMed:22914218] ##WORLDCAT## [DOI] (I p) - ↑ http://qualimap.bioinfo.cipf.es
