> ## Documentation Index > Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt > Use this file to discover all available pages before exploring further. # Bulk RNAseq Quantification Walkthrough ## Upload your RNAseq data Use the ‘Upload’ modal found on the top right, and upload your raw .fastq or .fastq.gz files to Latch Data with the upload modal. ### Set up samplesheet on Latch Registry Create new Project (if needed) and a new Sheet under that Project for the experiment being run. ### Launch ‘nf-core/rnaseq’ Latch Workflow Choose the ‘nf-core/rnaseq’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it). Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata. Or choose your own Reference FASTA and GTF in the ‘Custom Reference Genome’ tab. Do not use spaces in the Run Name. We recommend leaving the Output Directory to its default location. (Optional - Advanced) Choose other parameters in ‘Optional Arguments’. There are descriptions for every parameter available when you hover above the (i) symbol on a parameter name. Double click the execution to be taken to detailed logs. Useful outputs are the run HTML report and all the computational outputs in the folder that matches the name of the aligner you used. ## Differential Gene Expression ### Launch ‘DESeq2 (Differential Expression)’ Latch Workflow Choose the ‘DESeq2 (Differential Expression)’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it). All outputs from ‘nf-core/rnaseq’ have an output folder called ‘deseq2\_counts’ with a TSV file that is the optimal input for DESeq2. Or choose advanced conditions for your samples in the ‘File/Registry’ tab through Latch Data or Latch Registry. We recommend leaving the Output to its default location. ### Visualize differential gene expression outputs in Latch Plots Choose the ‘Differential Gene Expression Visualizer (0.0.6)’ template. Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata. ## Pathway Enrichment ### Launch ‘Pathway Enrichment Analysis’ Latch Workflow Choose the ‘Pathway Enrichment Analysis’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it). Each run will have a ‘Data/Contrast’ folder with a file for every comparison created in DESeq2.