Up: Component summary
Up: Component summary
Component
Bam2CountsConverts 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) |
| Issue tracker | View/Report issues |
| 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 |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | Array<BAM> | Mandatory | Array of BAM files for which counts are calculated. |
Outputs| Name | Type | Description |
|---|---|---|
| out | CSV | Matrix of counts for each entity. |
Parameters| 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 in |
OUT out |
|||
|---|---|---|---|---|---|---|
| case1 | properties | in | (missing) | |||
|
entityList=ENST00000335137,ENST00000450305 |
||||||