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base repository: hdesai17/chemoproteogenomics
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head repository: BackusLab/chemoproteogenomics
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Commits on Jan 6, 2025

  1. New Google Drive link

    hdesai17 authored Jan 6, 2025

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Showing with 2 additions and 2 deletions.
  1. +2 −2 README.md
4 changes: 2 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
@@ -33,7 +33,7 @@ git clone https://github.com/hdesai17/chemoproteogenomics.git
```

2. Move VCF file into the root directory (_../chemoproteogenomics_) or make sure the working directory contains VCF, Annotations/Tools folders and GenerateBD.sh script \
A sample VCF file is [here](https://drive.google.com/drive/folders/1w1EaQC7q5uVudEMCGo-zREVJhK-YOC13?usp=sharing)
A sample VCF file is [here](https://drive.google.com/drive/folders/0B3bUQnhSJGnxfmltTm5URlNhMUVZX2xfdEhwVHpjcFB3eVF1Y0tVSFVRSkdPTFB0N2w5YVk?resourcekey=0-Tz7BhL5bFDBs9w0jUB2kVQ&usp=drive_link)

>[!IMPORTANT]
>The VCF has should have file name format SAMPLE_NAME_RNA.vcf or SAMPLE_NAME_Exome.vcf \
@@ -43,7 +43,7 @@ git clone https://github.com/hdesai17/chemoproteogenomics.git
mv *.vcf chemoproteogenomics
```

3. Download Genocode v28 protein coding translations and GTF annotation files as well as RData file of common missense SNPs [from this link](https://drive.google.com/drive/folders/1w1EaQC7q5uVudEMCGo-zREVJhK-YOC13?usp=sharing) and move all three into Annotations directory
3. Download Genocode v28 protein coding translations and GTF annotation files as well as RData file of common missense SNPs [from this link](https://drive.google.com/drive/folders/0B3bUQnhSJGnxfmltTm5URlNhMUVZX2xfdEhwVHpjcFB3eVF1Y0tVSFVRSkdPTFB0N2w5YVk?resourcekey=0-Tz7BhL5bFDBs9w0jUB2kVQ&usp=drive_link) and move all three into Annotations directory

```
mv *gencode /path/to/working/directory/Annotations/