Count the reads overlapping the exonic counting bins of a DEXSeq annotation
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
bam
:file
BAM file of the aligned reads, sorted by position. For a BAM sorted
by name, pass --order name through ext.args; a mismatched sort
order gives wrong counts without any error.
*.bam
meta2
:map
Groovy Map containing annotation information
e.g. [ id:'genome' ]
gff
:file
Flattened DEXSeq annotation, as created by dexseq/prepareannotation
*.gff
Output
name:type
description
pattern
counts
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
