From 5e1f1107f911d6d1ca21163333908acb75251e9d Mon Sep 17 00:00:00 2001 From: inemesb Date: Fri, 7 Nov 2025 11:43:33 +0100 Subject: [PATCH] Add test background profile for methbat --- README.md | 2 ++ .../pacbio/tsv/methbat_background_profile_small.tsv | 7 +++++++ 2 files changed, 9 insertions(+) create mode 100644 data/genomics/homo_sapiens/pacbio/tsv/methbat_background_profile_small.tsv diff --git a/README.md b/README.md index 11033bb17..22542eed0 100644 --- a/README.md +++ b/README.md @@ -622,6 +622,8 @@ The earth sciences folder contain subfolders for different data formats encounte - alz.ccs.fastq: CCS reads generated using pbccs on alz.bam in fastq format - alz.ccs.fastq.gz: CCS reads generated using pbccs on alz.bam in gziped fastq format - test_hifi.fastq.gz: Reads mapping to a randomly selected contig from the whole genome assembly by [Cheng et al., 2021](https://www.nature.com/articles/s41592-020-01056-5) of the child of the GIAB Ashkenazim trio [RM8392](https://www-s.nist.gov/srmors/view_detail.cfm?srm=8392). The reads were taken from [SRR10382244](https://www.ncbi.nlm.nih.gov/sra/?term=SRR10382244). + - tsv: + - methbat_background_profile_small.tsv: background profile for methbat, with two regions and three labels based on reads in 'NA037562_downsampled.pbmm2.repeats.phased.bam'. - txt: - filelist.txt: A TAMA merge filelist file. It's a 4 columns (bed file, cap status, merging order, id) file listing bed files to merge. The file listed are alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed. - vcf: diff --git a/data/genomics/homo_sapiens/pacbio/tsv/methbat_background_profile_small.tsv b/data/genomics/homo_sapiens/pacbio/tsv/methbat_background_profile_small.tsv new file mode 100644 index 000000000..8e2f9b23e --- /dev/null +++ b/data/genomics/homo_sapiens/pacbio/tsv/methbat_background_profile_small.tsv @@ -0,0 +1,7 @@ +chrom start end data_category num_phased num_unphased NoData Uncategorized Methylated Unmethylated AlleleSpecificMethylation avg_abs_meth_deltas stdev_abs_meth_deltas avg_combined_methyls stdev_combined_methyls +chr19:45760000-45770300 8000 10000 ALL 72 3 0 0 75 0 0 0.036903112 0.028632843 0.937348504 0.027318566 +chr19:45760000-45770300 8000 10000 FEMALE 43 2 0 0 45 0 0 0.039704932 0.030229108 0.939890471 0.026852558 +chr19:45760000-45770300 8000 10000 MALE 29 1 0 0 30 0 0 0.03274869 0.026043223 0.933535552 0.028022734 +chr19:45760000-45770300 10000 12000 ALL 73 2 0 0 0 75 0 0.022414432 0.01890777 0.147347258 0.013668171 +chr19:45760000-45770300 10000 12000 FEMALE 44 1 0 0 0 45 0 0.020671169 0.019389695 0.151474917 0.01162018 +chr19:45760000-45770300 10000 12000 MALE 29 1 0 0 0 30 0 0.025059382 0.018163335 0.141155769 0.014343825 \ No newline at end of file