README.md

PigHeaT RRBS analysis

Analysis of PigHeaT RRBS data.

Whole-blood samples were taken form back-cross pigs Large White x (Large White x Créole pigs) that were raised in either a temperate or a tropical facility.

Reads were processed by Sonia using Remi's RRBS pipeline: private link to pipeline

01. metadata cleaning

Link to script

Over the 479 initial RRBS samples, one file was not successfully processed (over-covered, not enough allocated compute ressources). Two fruther libraries had 0 CpG sites covered with at least 10 reads: GC45472 and URZ3149. Metadata was gathered from the PigHeaT sharepoint for the remainig 476 samples, leading to this metadata table.

02. BED import into a BSseq object

Link to script

BED import into a BSseq object was performed on the GenoBioinfo cluster as following: