Difference between revisions of "Qualimap"
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* optparse (available from CRAN) | * optparse (available from CRAN) | ||
* NOISeq, Repitools, Rsamtools, GenomicFeatures, rtracklayer (available from Bioconductor) | * NOISeq, Repitools, Rsamtools, GenomicFeatures, rtracklayer (available from Bioconductor) | ||
| + | |||
| + | = Usage = | ||
| + | |||
| + | On its own, the GUI will be launched. | ||
| + | |||
| + | However if you launch | ||
| + | |||
| + | qualimap bamqc -bam <bamfile> -outfile <youpdfname.pdf> | ||
| + | |||
| + | it seems to know it should behave in command-line fashion | ||
| + | |||
| + | Typical output (truncated) | ||
| + | Processed 400 out of 403 windows... | ||
| + | Total processed windows:403 | ||
| + | Number of reads: 790595 | ||
| + | Number of valid reads: 72116 | ||
| + | Number of correct strand reads:0 | ||
| + | |||
| + | Inside of regions... | ||
| + | Num mapped reads: 72116 | ||
| + | Num mapped first of pair: 36084 | ||
| + | Num mapped second of pair: 36032 | ||
| + | Num singletons: 1216 | ||
| + | Time taken to analyze reads: 159 | ||
| + | Computing descriptors... | ||
| + | numberOfMappedBases: 14882078 | ||
| + | referenceSize: 3359974 | ||
| + | numberOfSequencedBases: 14876535 | ||
| + | numberOfAs: 4618823 | ||
| + | Computing per chromosome statistics... | ||
| + | Computing histograms... | ||
| + | Overall analysis time: 160 | ||
| + | end of bam qc | ||
| + | Computing report... | ||
| + | Writing PDF report... | ||
| + | PDF file created successfully | ||
| + | |||
| + | If you used the '''-outfile''' option, It creates a directory where is will put a pdf file, and a txt file. The name of the directory is usualy the root name of the bamfile. | ||
= Links= | = Links= | ||
* [http://qualimap.bioinfo.cipf.es/doc_html/intro.html#citing-qualimap homepage] | * [http://qualimap.bioinfo.cipf.es/doc_html/intro.html#citing-qualimap homepage] | ||
Latest revision as of 23:07, 27 April 2017
Contents
Introduction
Inspecting bam files for quality. Comes from same home as Blast2Go, the famous functional annotation system, in CIPF, Valencia, Spain.
Installation
Has a number of dependencies:
- optparse (available from CRAN)
- NOISeq, Repitools, Rsamtools, GenomicFeatures, rtracklayer (available from Bioconductor)
Usage
On its own, the GUI will be launched.
However if you launch
qualimap bamqc -bam <bamfile> -outfile <youpdfname.pdf>
it seems to know it should behave in command-line fashion
Typical output (truncated) Processed 400 out of 403 windows... Total processed windows:403 Number of reads: 790595 Number of valid reads: 72116 Number of correct strand reads:0 Inside of regions... Num mapped reads: 72116 Num mapped first of pair: 36084 Num mapped second of pair: 36032 Num singletons: 1216 Time taken to analyze reads: 159 Computing descriptors... numberOfMappedBases: 14882078 referenceSize: 3359974 numberOfSequencedBases: 14876535 numberOfAs: 4618823 Computing per chromosome statistics... Computing histograms... Overall analysis time: 160 end of bam qc Computing report... Writing PDF report... PDF file created successfully
If you used the -outfile option, It creates a directory where is will put a pdf file, and a txt file. The name of the directory is usualy the root name of the bamfile.
