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Added background profile tsv for methbat/profile #1778

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Merged
merged 2 commits into from
Nov 10, 2025
Merged

Added background profile tsv for methbat/profile #1778

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5e1f110
Add test background profile for methbat
inemesb Nov 7, 2025
e466ad1
Merge branch 'nf-core:modules' into modules
inemesb Nov 7, 2025
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -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:
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7 changes: 7 additions & 0 deletions data/genomics/homo_sapiens/pacbio/tsv/methbat_background_profile_small.tsv
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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