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Fixing the internal links in README.md #77

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Fixing the internal links in README.md #77

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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -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 *\<PARENT_DIR\>, \<SIFT4G_PATH\>, \<PROTEIN_DB\>*
[(See config details)](#configFile) . Be sure to use __full paths__
[(See config details)](#configuration-file) . Be sure to use __full paths__

`mkdir <PARENT_DIR>`

Expand All @@ -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 *\<PARENT_DIR\>/\<ORG_VERSION\>*.

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

Expand Down Expand Up @@ -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 *\<PARENT_DIR\>/\<ORG_VERSION\>*.

3. [Check the database](#checkDB)
3. [Check the database](#check-the-database)

## Usage

Expand All @@ -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*

Expand All @@ -112,7 +112,7 @@ MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial

`perl make-SIFT-db-all.pl -config <config file> --ensembl_download`

3. [Check the database](#checkDB)
3. [Check the database](#check-the-database)

4. [Annotate a VCF file with your database](#annotate)

Expand All @@ -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: *\<DBSNP_VCF_FILE\>*

[See config details](#configFile).
[See config details](#configuration-file).

2. Put the genomic fasta files and the gene annotation files in their proper place:

Expand Down Expand Up @@ -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)

Expand Down