Tag: ChromHMM

ChromHMM | SCAI

ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence…

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Bioconductor – chromhmmData

DOI: 10.18129/B9.bioc.chromhmmData     Chromosome Size, Coordinates and Anchor Files Bioconductor version: Release (3.14) Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two…

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DNA methylation EPIC array and ChromHMM

DNA methylation EPIC array and ChromHMM 0 Hello, I have DNA methylation data obtained by the EPIC array and I would like to use this data to check for chromatin states using the ChroHMM software. I understand that the data must be in a binary format, grouped by each 200bp,…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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