I am trying to fetch variant details, including **population allele frequency (`af`)**, from the gnomAD database using the GraphQL API. However, the query does not …

Hi all, I am trying to learn some snakemake workflows. I would like to ask is there anyway to colorize the text in Snakemake as …

Hi all, I am trying to use GATK mutect2/haplotype (default option) for variant calling on a bam file from single-cell RNAseq data; however, the generated …

Hi all, I would like to download database from this website: https://sorfs.ugent.be/database but it seems that they do not maintain the database anymore, only the …

Hi All, I try to import an mtx file (with features and barcode) as scanpy objects: `adata= sc.read_10x_mtx(data_dir, var_names='gene_symbols', cache=True)` however, an error occurs: (path)/envs/sc/lib/python3.11/site-packages/anndata/_core/anndata.py:1908: …

Hello everyone, I am trying to build a new database in snpEff. I have followed all the steps given in manual. But, unfortunately could not …

Hi I am new to this forum and bioinformatics, I am trying to understand the functionality of the VariantAnnotation package in Bioconductor R, in the …

Hi, I am using karyoploteR to visualize CNV. I am getting following error. But I do have the genomic region in a bed file. Could …

I am using the RNA-seq workflow: gene-level exploratory analysis and differential expression. I have summerizeoverlap output 0 so <- summarizeOverlaps(ebg, "Epigenomics02-96.alignments.bam", mode="Union", + singleEnd=FALSE, + …

Hi, I'm trying to merge these two bam files and I did the command samtools merge merged.bam file1.bam file2.bam However, it gives me this error: …