I have 10x Genomics scRNA-seq data processed through CellRanger. I now have the filtered_feature_bc_matrix output. What is the complete Seurat workflow from loading data to…
I keep seeing TPM, FPKM, and RPKM used in RNA-seq papers and tools. What is the mathematical difference between them? Which should I use for…
I ran DESeq2 and got a list of differentially expressed genes with log2 fold changes and adjusted p-values. Now I want to understand what biological…
I ran a BLAST search and got hits with E-values like 2e-45, 0.003, and 12. I understand lower is better, but what does the E-value…
I have 50 novel protein sequences from a genome annotation and want to predict their 3D structures. I don’t have access to expensive cloud GPU…
I want to build a RNA-seq analysis pipeline that I can share with collaborators and rerun on different datasets without manually changing paths. I’ve heard…
I have 10x Genomics Visium spatial transcriptomics data from mouse brain tissue. The CellRanger Space output is ready. I want to visualize gene expression on…
I need to align paired-end RNA-seq reads to the human GRCh38 reference genome using STAR. What are the steps to: (1) generate the genome index,…
I’m doing differential expression analysis with DESeq2 in R. I have raw count data from featureCounts. Should I normalize the counts before passing them to…
I keep running into dependency conflicts when installing bioinformatics tools. Different tools require different Python versions and library versions. How should I use conda environments…
I’m trying to run a germline variant calling pipeline on whole-genome sequencing data. I have BWA-MEM2 aligned and sorted BAM files. What is the correct…
I have an unsorted BAM file from a BWA-MEM alignment. I need to: (1) sort and index it, (2) filter out unmapped and low-quality reads,…
I’m integrating scRNA-seq datasets from 3 different batches (different labs, same tissue type). After merging in Seurat, the UMAP clusters by batch rather than by…
I have paired-end Illumina RNA-seq data and I need to trim adapters and low-quality bases before alignment. I’ve been told to use Trimmomatic but I’m…
I have a multi-sequence FASTA file with 50,000 protein sequences. I want to: (1) filter sequences by length (keep only 100–500 aa), (2) calculate amino…
