Up: Component summary
Up: Component summary
Function
HTSeqBam2CountsFor obtaining read counts at gene and exon level from RNA-Seq alignment files
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Alejandra Cervera (alejandra.cervera@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| alignments | Array<BinaryFile> | Mandatory | The aligned RNA-seq reads in BAM or SAM format. |
| annotationGTF | GTF | Optional | Gene annotation file in GTF format. |
| annotationGFF | GFF | Optional | Gene annotation file in GFF format as required by DEXSeq (only for needed for exon counts). If not defined then annotationGTF will be converted to GFF and it will become available as the annotation output. |
Outputs| Name | Type | Description |
|---|---|---|
| exon | Array<TextFile> | Array of exon counts for each alignment file. |
| gene | Array<TextFile> | Array of gene counts for each alignment file. |
| annotation | GFF | Annotation in GFF format |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| dexseq_dir | string | "/opt/DEXSeq/inst/python_scripts/" | Directory where the dexseq_count.py and dexseq_prepare_annotation.py are located |
| entity | string | "Exon" | Level at which the counts are required: possible values are "Exon,Gene", "Exon" or "Gene". |
| format | string | "bam" | Either bam or sam. |
| sorted | boolean | false | set to true if the bam/sam alignments are sorted by read name |
Test cases| Test case | Parameters▼ | IN alignments |
IN annotationGTF |
IN annotationGFF |
OUT exon |
OUT gene |
OUT annotation |
|---|---|---|---|---|---|---|---|
| case_exon | (missing) | alignments | (missing) | annotationGFF | exon | (missing) | annotation |
| case_gene | properties | alignments | annotationGTF | (missing) | (missing) | gene | annotation |
|
# Test case gene, |
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