Require snvboxGenes.fa file

[vivekruhela]

Hello,

I am using the 2020+ tool to identify the potential candidate driver gene. I can download the required files, such as snvboxGenes.bed or scores.tar.gz, but I am not able to get the exact file required for gene.fa in the following command:

mut_annotate --summary -i genes.fa -b genes.bed -s score_dir -m mutations.txt -o summary.txt

I tried various fasta files generated from UCSC Table Brower, but now of them worked. Can you share the exact fasta file you used in your published work? Thanks.

[ctokheim]

Hi. The snvboxGenes.fa file (i.e. input of -i in mut_annotate) is generated from the extract_gene_seq command (see https://probabilistic2020.readthedocs.io/en/latest/tutorial.html#gene-fasta). One just needs to download the hg19 fasta file from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit), convert the file from 2bit to fasta format using the twoBitToFa command line tool from UCSC, and then run extract_gene_seq command with hg19.fa and snvboxGenes.bed as input.

I've also attached the snvboxGenes.fa file below as well. snvboxGenes.fa.gz