News.rst and documentation

maxplanck-ie · Apr 9, 2024 · e221ebd · e221ebd
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diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -6,6 +6,7 @@ ________________
 
 * added SEACR peaks qc
 * added external bed functionality for differential binding in ChIP-seq and ATAC-seq workflows
+* added "allelic-counting" mode to mRNA-seq, allowing to count reads and run DGE from allelic bam files split e.g. by whatshap
 * fixed copyfile command for sampleSheet
 * removed deprecated --force argument from mamba commands
 * fixes #998

diff --git a/docs/content/workflows/mRNA-seq.rst b/docs/content/workflows/mRNA-seq.rst
@@ -194,6 +194,11 @@ Allele-specific, gene-level differential expression analysis is then performed u
 
 .. note:: **allelic-mapping** mode is mutually exclusive with **mapping** mode
 
+"allelic-counting"
+~~~~~~~~~~~~~~~~~~
+
+**allelic-counting** mode requires the user to input, per sample, 4 bam files, corresponding to haplotype1, haplotype2, unassigned and haplotagged , e.g. as generated by whatshap. The respective suffixes ".genome1", ".genome2", ".unassigned", ".alelle_flagged" are required to be followed by the bam extention ".sorted.bam". This mode is mutually exclusive with "deepTools_qc". Only the allelic version of deepTools qc will be run, by default. Allelic version of featureCounts will be run by default. If sample sheet is provided, allelic DESeq2- or allelic Salmon-based differential gene expression analysis will be run. 
+
 "alignment-free"
 ~~~~~~~~~~~~~~~~