User: danielcgingerich

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Posts by danielcgingerich

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HOMER Motif Analysis code not working
... I am trying to do motif analysis on a set of ATAC peaks with `findMotifsGenome.pl` using HOMER installed on a computer cluster. I submit a simple slurm job: #!/bin/bash #SBATCH -J HOMER.test #SBATCH -o %A_%a.out.txt #SBATCH -e %A_%a.err.txt #SBATCH --mem=24G #SBATCH -n 8 ...
genome bioinformatics rna-seq written 6 weeks ago by danielcgingerich0
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Confused about sequence motif regular expressions
... Consider the regular expression for this motif: A, followed by anything but C, followed by either A or T, followed by G.... i.e.: A{C}[AT]G Is this regular expression used to describe variation in motifs across individuals, or within individuals? For example, if I have this motif in my own DNA ...
genome genetics rna-seq written 7 weeks ago by danielcgingerich0 • updated 7 weeks ago by Mensur Dlakic8.9k
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biomaRt not finding all genes
... I need to align a dataset mapped to GRCh38.p2 (ensembl 79) and a dataset mapped to GRCh38.p13 (ensembl 98). The first dataset (ensembl 79) has gene names and entrez IDs. The second dataset (ensembl 98) has gene names and ENSG IDs. I want to convert ensembl 79 entrez IDs to ENSG IDs. When I query on ...

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