SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta

Steps to generate the files in this data source:<br>1 - Clone the git repository at github.com/XuegongLab/neoguider and install according to the instructions on the github website. <br>2 - Download and extract the fastq files with accessions SRR7890830, SRR7890845, and SRR9134697; then, put the fastq files into the testdata directory.3 - run the following (this should take about three hours with 16 CPUs), you can go to the next step if you have manually put the corresponding file from this data source into testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta<br>snakemake --configfile config.yaml --config res=testdata/results_from_fastq/ prefix=SRR7890830-SRR7890845-SRR9134697 dna_tumor_fq1=testdata/SRR7890830_1.fastq.gz dna_tumor_fq1=testdata/SRR7890830_2.fastq.gz dna_normal_fq1=testdata/SRR7890845_1.fastq.gz dna_normal_fq2=testdata/SRR7890845_2.fastq.gz rna_tumor_fq1=testdata/SRR9134697_1.fastq.gz rna_tumor_fq2=testdata/SRR9134697_2.fastq.gz <br>4 - run the following (this should take about one hour with 16 CPUs)<br>snakemake --printshellcmd --configfile config.yaml --config res=testdata/results_from_fasta prefix=SRR7890830-SRR7890845-SRR9134697 tumor_spec_peptide_fasta=testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta5 - Finally, you will see the SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta and SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv files in the directory testdata/results_from_fastq. <br>The file SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv also appears in testdata/results_from_fasta if you prioritized with tumor_spec_peptide_fasta as input. <br><br>