NARWHAL
NARWHAL — Neoantigens Recognition Website and HLA Genotyping Tool
Start Neoantigen Start HLA typing
Overview
Congradulations! Your job has been completed successfully!
The followings are details about your job and logs/results. Please click the left navigation panel to show results of each step.
Information about your job:
| Job ID | 66b1d000b948119948956a597fa8050268b89fb23bb73085b8a622e4d945050e |
| Submission time | April 17, 2024, 4:37 a.m. |
| Start time | April 17, 2024, 4:37 a.m. |
| End time | April 17, 2024, 3:57 p.m. |
| Download the TSA candidate file (TSV format) | Download |
Quality Control
Quality Control (QC) Result
The following results include FastQC files and MultiQC files for both tumor and normal samples.
QC report links: Tumor R1
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FastQC before trimming | raw reads | |
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FastQC after trimming | paired reads | unpaired reads |
QC report links: Tumor R2
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FastQC before trimming | raw reads | |
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FastQC after trimming | paired reads | unpaired reads |
QC report links: Normal R1
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FastQC before trimming | raw reads | |
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FastQC after trimming | paired reads | unpaired reads |
QC report links: Normal R2
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FastQC before trimming | raw reads | |
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FastQC after trimming | paired reads | unpaired reads |
Tumor Trimmomatic
| log file |
Normal Trimmomatic
| log file |
Mutation Calling and Annotation
Mutation and Annotation Result
The following results include: (1) VCF files generated by VarScan, (2) a HTML, a VCF file , a TXT file, and a summary report of somatic mutations obtained from VEP annotation, and (3) a HTML, a VCF file , a TXT file, and a summary report of germline mutations obtained from VEP annotation.
Mutations (VarScan)
| T.somatic.mutation.vcf | T.germline.mutation.vcf |
Annotated Somatic Mutations
| T.somatic.summary.html | T.annotated.somatic.vcf | T.annotated.somatic.txt |
Annotated Germline Mutations
| T.germline.summary.html | T.annotated.germline.vcf | T.annotated.germline.txt |
RNA Expression Level Calculation and Filtering
RNA Expression Level Result
The following results include: (1) RNA expression levels of filtered TSA cantididates (tumor TPM > threshold [default: 1.0]) (2) RNA expression levels of all identified TSA cantididates (2) RNA expression levels of all genes in tumor, and (3) RNA expression levels of all genes in normal.
RNA expression levels of filtered TSA cantididates
| filtered.peptides.tpm.tsv |
RNA expression levels of all identified TSA cantididates
| peptides.tpm.tsv |
RNA expression levels of all genes
| tumor.abundance.tsv | normal.abundance.tsv |
TSA Identification with RNA-seq
TSA Identification Report
The following files represent mTSA and aeTSA reports under various filtered conditions.
Total TSA Result (in TSV format): Download
mTSA Result (in TSV format): Download
mTSA Result (in FASTA format): Download
aeTSA Result (in TSV format): Download
aeTSA Result (in FASTA format): Download
Validation of TSAs with LC-MS/MS Peptides