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Merge pull request #25 from ZKai0801/master
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Update README.md
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sfchen authored May 21, 2020
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Expand Up @@ -89,6 +89,11 @@ Notes:
If you'd like to create a custom fusion file, you can use `scripts/make_fusion_genes.py`
As the script uses `refFlat.txt` file to determine genomic coordinates of exons, you need to download a `refFlat.txt` file from UCSC Genome Browser in advance. Of course, the choice of using either hg19 or hg38 is up to you.

- For hg19: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
- For hg38: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz

Please make sure unzip the file to txt format before you continue

As for the input gene list file, all genes should be listed in separate lines. By default, the longest transcript will be used. However, you can specify a different transcript by adding the transcript ID to the end of a gene. The gene and its transcript should be separated by a tab or a space. Please note that each gene should be the HGNC official gene symbol, and each transcript should be NCBI RefSeq transcript ID.

An example of gene list file:
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