diff --git a/README.md b/README.md index 49640d4ae..730b7bf24 100644 --- a/README.md +++ b/README.md @@ -708,6 +708,11 @@ The earth sciences folder contain subfolders for different data formats encounte - test2.sorted.bam.bai: Index for test2.sorted.bam - test.sorted.phased.bam: Haplotagged version of test.sorted.bam - test.sorted.phased.bam.bai: Index for test.sorted.phased.bam + - bedmethyl + - test_hp1.bed.gz: bgzip-compressed bedMethyl pileup for haplotype 1 of test.sorted.phased.bam, generated with `modkit pileup --phased --modified-bases 5mC 5hmC` against genome.fasta, for testing modkit/dmr + - test_hp1.bed.gz.tbi: Tabix index for test_hp1.bed.gz + - test_hp2.bed.gz: bgzip-compressed bedMethyl pileup for haplotype 2 of test.sorted.phased.bam, generated the same way as test_hp1.bed.gz + - test_hp2.bed.gz.tbi: Tabix index for test_hp2.bed.gz - HG002_ont_telomere - HG002_ont_tel_sub.bam: 17 ONT telomeric reads from [GIAB HG002 2025.01 release](https://ont-open-data.s3.amazonaws.com/giab_2025.01/basecalling/sup/HG002/PAW70337/calls.sorted.bam) (SUP basecalling, R10.4.1). Regions: last 10 kb of chr1 and chr2, downsampled with `samtools view -s 42.12`. - HG002_ont_tel_sub.bam.bai: Index for HG002_ont_tel_sub.bam diff --git a/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz new file mode 100644 index 000000000..fd3e24202 Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz differ diff --git a/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz.tbi b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz.tbi new file mode 100644 index 000000000..cb82c5b8f Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp1.bed.gz.tbi differ diff --git a/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz new file mode 100644 index 000000000..dbabf80c1 Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz differ diff --git a/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz.tbi b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz.tbi new file mode 100644 index 000000000..a32907fe1 Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bedmethyl/test_hp2.bed.gz.tbi differ