diff --git a/README.md b/README.md index fb12179ae..aa87355bf 100644 --- a/README.md +++ b/README.md @@ -32,6 +32,38 @@ git remote set-branches --add origin [remote-branch] git fetch ``` +## Test Dataset Overview + + +- Source: ENCODE Mouse Development Matrix + + - DOI: https://doi.org/10.1038/nature11247 + +- Tissue: Kidney + +- Stage: Postnatal Day 0 (P0) + +- Replicate: 1 + +- Marks/Assays: H3K4me3 (ChIP-seq), H3K36me3 (ChIP-seq), WGBS + +- Files: + - https://www.encodeproject.org/files/ENCFF824RZT/@@download/ENCFF824RZT.bam -> H3K4me3 + - https://www.encodeproject.org/files/ENCFF980SRC/@@download/ENCFF980SRC.bam -> H3K36me3 + - https://www.encodeproject.org/files/ENCFF847ROX/@@download/ENCFF847ROX.bed.gz -> WGBS + +```bash +# 1. Subset to chr12 +samtools view -b H3K4me3_KIDNEY_MOUSE_P0.bam chr12 > H3K4me3_KIDNEY_MOUSE_P0_chr12.bam +zcat WGBS_KIDNEY_MOUSE_P0.bed.gz | awk '$1 == "chr12"' | gzip > WGBS_KIDNEY_MOUSE_P0_chr12.bed.gz + +# 2. Downsample to specific 500kb region +samtools view -h -b H3K4me3_KIDNEY_MOUSE_P0_chr12.bam "chr12:10000000-10500000" > small_H3K4me3.bam +samtools view -h -b H3K36me3_KIDNEY_MOUSE_P0_chr12.bam "chr12:10000000-10500000" > small_H3K36me3.bam +zcat WGBS_KIDNEY_MOUSE_P0_chr12.bed.gz | awk '$1=="chr12" && $2>=10000000 && $3<=10500000' | gzip > small_WGBS.bed.gz +``` + + ## Support For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging). diff --git a/testdata/H3K36me3_mm10_kidney_chr12_reduced.bam b/testdata/H3K36me3_mm10_kidney_chr12_reduced.bam new file mode 100644 index 000000000..2afe6016e Binary files /dev/null and b/testdata/H3K36me3_mm10_kidney_chr12_reduced.bam differ diff --git a/testdata/H3K4me3_mm10_kidney_chr12_reduced.bam b/testdata/H3K4me3_mm10_kidney_chr12_reduced.bam new file mode 100644 index 000000000..5fa421e56 Binary files /dev/null and b/testdata/H3K4me3_mm10_kidney_chr12_reduced.bam differ diff --git a/testdata/WGBS_mm10_kidney_chr12_reduced.bed.gz b/testdata/WGBS_mm10_kidney_chr12_reduced.bed.gz new file mode 100644 index 000000000..66daf78b7 Binary files /dev/null and b/testdata/WGBS_mm10_kidney_chr12_reduced.bed.gz differ