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All tools and services of BV-BRC

Abstract: Genomics * Genome Assembly * Genome Annotation * Comprehensive Genome Analysis (B) * BLAST * Primer Design * Similar Genome Finder * Genome Alignment * Variation Analysis *

Variant calling (inter-host + intra-host) for Data_Pietschmann_229ECoronavirus_Mutations_2025 (via docker own_viral_ngs) v2

Author: gene_x

Abstract: 1. Input data: ln -s ../raw_data_2024/hCoV229E_Rluc_R1.fastq.gz hCoV229E_Rluc_R1.fastq.gz ln -s ../raw_data_2024/hCoV229E_Rluc_R2.fastq.gz hCoV229E_Rluc_R2.fastq.gz ln -s ../r

How to correlate RNA-seq Data with Mass Spectrometry Proteomics Data?

Author: gene_x

Abstract: Correlating RNA-seq data with mass spectrometry (MS)-based proteomics data is a powerful way to link transcript-level expression with protein-level abundance. Here’s a step-by-step outline of how to a

Workflow using QIIME2 for Data_Marius_16S_2025

Author: gene_x

Abstract: 1. Install and test qiime2-docker #Cannot run under QIIME1, switch to QIIME2: pick_open_reference_otus.py -r/home/jhuang/REFs/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_

Processing Data_Tam_RNAseq_2025_LB_vs_Mac_ATCC19606

Author: gene_x

Abstract: 1. Targets Could you please assist me with processing RNA-seq data? The reference genome is CP059040. I aim to analyze the data using PCA, a Venn diagram, and KEGG and GO annotation enrichmen

How to debug and construct the docker docker own_viral_ngs?

Author: gene_x

Abstract: mkdir viralngs; cd viralngs ln -s ~/Tools/viral-ngs_docker/Snakefile Snakefile ln -s ~/Tools/viral-ngs_docker/bin bin cp ~/Tools/viral-ngs_docker/refsel.acids refsel.

Variant calling for Data_Pietschmann_229ECoronavirus_Mutations_2025 (via docker own_viral_ngs)

Author: gene_x

Abstract: 1. Input data: ln -s ../raw_data_2024/hCoV229E_Rluc_R1.fastq.gz hCoV229E_Rluc_R1.fastq.gz ln -s ../raw_data_2024/hCoV229E_Rluc_R2.fastq.gz hCoV229E_Rluc_R2.fastq.gz ln -s ../r

Post-processing of DAMIAN results

Author: gene_x

Abstract: 1. Prepare input raw data # -- Ringversuch -- ~/DATA/Data_Damian/241213_VH00358_120_AAG523FM5_Ringversuch ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R

Analysis of the RNA binding protein (RBP) motifs for RNA-Seq and miRNAs (v3)

Author: gene_x

Abstract: There are several alternative R packages and tools to perform motif enrichment analysis for RNA-binding proteins (RBPs), beyond PWMEnrich::motifEnrichment(). Here are the most notable ones: | Too

Visualization and Export of miRNA Expression Profiles Using Manhattan Plots in R

Author: gene_x

Abstract: This R script processes raw miRNA read count data to visualize expression profiles across different samples using Manhattan plots. The main steps include: * Normalization: Raw counts are converted to