bethanystone/ngs-scripts

Scripts for next generation sequencing analyses forked from Diep (dtrain16/NGS-scripts)

NGS-scripts

Repository for scripts used for analysing next generation sequencing data (described in order below).

100bp_dmr_merge.r

Supplemental script for 100bp_dmrs.v0.1.sh for collapsing/summarising DMRs

100bp_dmrs.v0.1.sh

This script uses 100bp windowed methylation data to call differences across the genome in a defined context with required coverage and a defined difference. These are performed in a pairwise manner between all samples of interest.

100bp_heatmap.sh

Uses the output from 100bp_dmrs.v0.1.sh to get mC from bed files (individual mC resolution).

100bp_wig_to_dmrs.r

First step of 100bp_dmrs.v0.1.sh that makes pairwise comparisons of windows showing a defined difference in a given context.

BS-SNPer.sh

Script to perform SNP calling from aligned bisulfite converted reads. Use on sorted BAM file.

C_context_window_SREedits.pl

DSS_calling.r

DSS_file_prep.r

RNAseq_DEGanalysis.sh

RNAseq_bam_to_100bpwigs.sh

RNAseq_bam_to_bedgraph.sh

RNAseq_bedgraph_to_bigwig_tdf.sh

RNAseq_v0.1.sh

TruSeq-adapters.fa

average_cov.sh

bed_to_rel_dist.sh

chip-seq_v0.1.sh

combined_wigs_to_PCA.r

conversion_rate_check.sh

dmr_merge.r

gene_to_gene_anno.sh

genome_wigs_heatmap.r

merge_covs.r

merge_wigs.r

met-sign.sh

methylation_tiling.sh

rel_methylation_plots-v2.r

rel_methylation_plots.r

repeat_methylation_plots.r

scatman_smooth.sh

smooth_scat.r

wgbs_cov_to_TDF.txt

wgbs_pipelinev0.4.sh

wgbs_wig_PCA.r