Up: Component summary Function

HTSeqBam2Counts

For 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)
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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,
entity=Gene,
sorted=true


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