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maxplanck-ie · Jan 13, 2025 · d73bace · d73bace
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diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,12 @@
 snakePipes News
 ===============
 
+snakePipes 3.1.1
+________________
+
+* added whatshap-allelic mode to mRNA seq
+
+
 snakePipes 3.1.0
 ________________
 

diff --git a/docs/content/workflows/mRNAseq.rst b/docs/content/workflows/mRNAseq.rst
@@ -94,6 +94,8 @@ There is a configuration file in ``snakePipes/workflows/mRNAseq/defaults.yaml``:
     # for allele-spcific mapping
     SNPFile:
     NMaskedIndex:
+    # for allelic-whatshap
+    pvcf:
     #### Flag to control the pipeline entry point
     fromBAM: False
     bamExt: '.bam'
@@ -202,6 +204,15 @@ Allele-specific, gene-level differential expression analysis is then performed u
 
 **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. 
 
+
+"allelic-whatshap"
+~~~~~~~~~~~~~~~~
+
+**allelic-whatshap** mode applies a standard alignment to a nonmasked genome with STAR, followed by allele-specific splitting
+of mapped files with whatshap, requiring a phased vcf file as input ( ``--phased-vcf`` ). Gene-level quantification is performed for each allele using **featureCounts**.
+Allele-specific, gene-level differential expression analysis is then performed using **DESeq2**.
+
+
 "alignment-free"
 ~~~~~~~~~~~~~~~~