Merge branch 'main' of https://github.com/gghill/thesis-RNAseq into main

README.md

@@ -9,8 +9,10 @@ Steps outlined in this repository:
 3. Adapter trimming with Bbduk
 4. Genome indexing and alignment with STAR
 5. Feature count with htseq-count
-6. Differential gene expression analysis
+6. Differential gene expression (DGE) analysis
    * identification of up and downregulated genes with DESeq2
    * conversion of genes to standardized UIDs with NCBI's eFetch Utility
    * annotation of biological processes and assignment of gene ontologies using FishEnrichr
    * visualization of GO pathways using simplifyEnrichment 
+
+Steps 1-5 can be found in the [pipeline](pipeline.md) while DGE is documented in the [DESeq2 markdown](DESeq2_markdown_GH_git_out.md)

pipeline.md

@@ -213,7 +213,7 @@ Dec 01 12:44:28 ..... started STAR run (short optimized)
 ---
 ## Differential Gene Expression
 Gene ID outputs from htseq take several forms. Many genes include a "LOC" prefix as a placeholder until orthologs have been verified. LOC genes required conversion prior to database querying. More stable identifiers exist as lower case letters and digits such as "coq10b" and "pck1". These forms are ready for querying by most databases and do not require conversion.
-After signficantly differentially expressed genes are identified (see [DESeq2 markdown](DESeq2.md)), they needed to be converted to a single format readable by a database, in this case the Maayan Lab [FishEnrichr](https://maayanlab.cloud/FishEnrichr/) database.
+After signficantly differentially expressed genes are identified (see [DESeq2 markdown](DESeq2_markdown_GH_git_out.md)), they needed to be converted to a single format readable by a database, in this case the Maayan Lab [FishEnrichr](https://maayanlab.cloud/FishEnrichr/) database.
 Conversion was done using the NCBI eFetch Utility and the following script
 ```bash
 #!/bin/bash