Skip to content
Permalink
479373775c
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

BAP_trophoblast_45X/README.md

Go to file
 
 
Cannot retrieve contributors at this time
12 lines (9 sloc) 786 Bytes
Raw Blame

BAP_trophoblast_45X

Following alignment (Hisat v2.2.1) of trimmed read pairs (cutadapt v2.7), and Gencode v38 feature quantification (featureCounts v2.0 in Rsubread package), alleles were phased using phaser.

For differential expression (DESeq2), count tables are processed via DESeq2_input_v03_TBLs_pass.R Analysis and plotting is performed via DESeq2_analysis_v04_TBLs_pass.R, which also calls AhernTBL_annotation_v01_pass.R to process additional annotations, and AE_analysis_v01_pass.R to call escapee genes.

Geneset enrichment analysis (GSEA) is performed via DESeq2_GSEA_TBLs_pass.R, and Weighted gene correlation network analysis (WGCNA) via WGCNA_DEG02_DTA_pass.R

For additional information please see the supplementary material at https://doi.org/10.1073/pnas.2211073119