Commit 76f3bb81 authored by domingue's avatar domingue

New feature: stranded count matrix

- added new argument
- if not option is given to `--library`, default is unstranded for backwards compatibility
- calls `dge_star_counts2matrixStranded` instead of `dge_star_counts2matrix`
- tests:
	+ 3 different options to `--library`
	+ not setting `--library`
	+ comparison with previous version.

Fixes #88
parent a7bf47fd
......@@ -35,6 +35,7 @@ Options:
--gtf <gtfFile> Custom gtf file instead of igenome bundled copy
--pc-only Use protein coding genes only for mapping and quantification
--disable-pe-pairing Disable auto-detection and pairing of paired end tracks
--library <library> Stranding protocol used for library preparation. Follows featureCounts conventions: 0, unstranded (default); 1, forward; 2, reverse
"""
//--star-params <extras> Extra parameters passed on to STAR
......@@ -53,6 +54,7 @@ val igenome = File(doArgs["igenome"])
val star_index = File(igenome, "Sequence/StarIndex")
val gtfFile = if (doArgs["gtfFile"] != null) File(doArgs["gtfFile"]) else File(igenome, "Annotation/Genes/genes.gtf")
val pePairingEnabled = !doArgs["disable-pe-pairing"]!!.toBoolean()
val libraryStrand = if (doArgs["library"] == null) "0" else doArgs["library"]
// does not work because of https://github.com/holgerbrandl/kscript/issues/98
//val extraStarParams = doArgs["star-params"] ?:
......@@ -189,6 +191,6 @@ evalBash("""
rend.R -e ${'$'}NGS_TOOLS/dge_workflow/star_qc.R .
# Condense counts into matrix
dge_star_counts2matrix
dge_star_counts2matrixStranded ${libraryStrand ?: ""}
""")
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