SexChrLab / Placenta_Sex_Diff

Sex differences in full term uncomplicated human placentas

Placenta_Sex_Diff

Sex differences in full-term, >= 36 weeks, uncomplicated human placentas

Sex differences in placenta expression

Step 1: Process RNA sequence data

• FastQC, MultiQC, and bamstats for visualizing quality. bbduk to trim reads and remove adaptors.
• Reads aligned to a GRCh38 sex chromosomome complement reference genome. See https://github.com/SexChrLab/XY_RNAseq for more details on aligning to a sex chromosomome complement reference genome
• Use the snakemake file rna.snakefile that includes the following steps:
• trimming, alignmnet, obtaining counts, and generating bam stats.
• see git clone git://github.com/SexChrLab/Placenta_Data_Processing.git for more details on data processing

Step 2: Run Limma/Voom

• Use the r file R_limmaVooom_placentaSexDiff.r that includes the following steps:
  • You will need a counts table generated from step 1 FeatureCounts and a pheno type file
  • run limma/voom