diff --git a/README.md b/README.md index 4dad955..e9447d4 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ Create genomic databases with SIFT predictions. Input is an organism's genomic D `cd test_files/candidatus_carsonella_ruddii_pv_config.txt` Edit the config file to set *\, \, \* - [(See config details)](#configFile) . Be sure to use __full paths__ + [(See config details)](#configuration-file) . Be sure to use __full paths__ `mkdir ` @@ -40,7 +40,7 @@ Create genomic databases with SIFT predictions. Input is an organism's genomic D It takes ~30 minutes for this database to be generated in *\/\*. -3. [Check the database](#checkDB) +3. [Check the database](#check-the-database) The database should be in a folder named something like: candidatus_carsonella_ruddii_pv/ASM1036v1.34 @@ -71,7 +71,7 @@ Files are already provided in [scripts_to_build_SIFT_db/test_files/homo_sapiens_ It takes ~2 hours for human chr21 and mitochondria predictions to be generated in *\/\*. -3. [Check the database](#checkDB) +3. [Check the database](#check-the-database) ## Usage @@ -92,7 +92,7 @@ This will download genome and gene files directly from Ensembl with the option _ a. Set weblinks to Ensembl genome and gene annotation files: *GENE_DOWNLOAD_SITE, PEP_FILE, CHR_DOWNLOAD_SITE* Optional: *DBSNP_ORGANISM_DOWNLOAD_SITE* - [Config file details](#configFile) + [Config file details](#configuration-file) b. Set output paths: *PARENT_DIR, ORG, ORG_VERSION* @@ -112,7 +112,7 @@ MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial `perl make-SIFT-db-all.pl -config --ensembl_download` -3. [Check the database](#checkDB) +3. [Check the database](#check-the-database) 4. [Annotate a VCF file with your database](#annotate) @@ -129,7 +129,7 @@ MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial Check *GENETIC_CODE_TABLE* and *MITO_GENETIC_CODE_TABLE* is set correctly. Optional to set: *\* - [See config details](#configFile). + [See config details](#configuration-file). 2. Put the genomic fasta files and the gene annotation files in their proper place: @@ -171,7 +171,7 @@ MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial `All done!` -4. [Check the database](#checkDB) +4. [Check the database](#check-the-database) 5. [Annotate a VCF file with your database](#annotate)