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Converts Bam files to count matrices summarizing on gene, transcript or exon level. Current implementation is unoptimized and should be used with caution.

A list of available inputDBs. A list of available inputTables.

Version 0.8
Bundle sequencing
Categories Convert
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Requires Rsamtools (R-bioconductor) ; GenomicFeatures (R-bioconductor) ; GenomicRanges (R-bioconductor) ; GenomicAlignments (R-bioconductor) ; rtracklayer (R-bioconductor)
Source files component.xml Bam2Counts.r
Usage Example with default values


Name Type Mandatory Description
in Array<BAM> Mandatory Array of BAM files for which counts are calculated.


Name Type Description
out CSV Matrix of counts for each entity.


Name Type Default Description
entity string "gene" Genomic feature according to which to summarize. One of 'gene', 'transcript' or 'exon'.
entityList string "" Comma separated list of transcript ids in inputDB type. Only fetch this subset from the inputDB database. By default fetches all entities.
ignoreStrands boolean true Ignore strands when counting read overlaps.
inputDB string "hg19" Name of UCSC input DB for database construction if no reference is supplied.
inputTable string "ensGene" Name of table defining the entity id type in the output.
reference string "" Path to the transcript database local SQLite copy. If not set, database is populated from UCSC on runtime (slow).

Test cases

Test case Parameters IN
case1 properties in (missing)


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