Alongside with the report, you may find directories called reference, and results.
Given a samples called YYY and a genome called XXX, the following files are present:
results/ ├── XXX.dna │ ├── Mapping │ | ├── YYY.bam │ | └── YYY.bam.bai | └── QC | ├── MultiQC_Mapping_data.zip | └── MultiQC_Mapping.html └── QC ├── MultiQC_FastQC_data.zip ├── MultiQC_FastQC.html ├── report_pe │ └── YYY.html └── report_se └── YYY.html
Alongside with this report, you may find a directory called reference. You shall find all requested files in it. By default, the following files are present:
reference/ ├── blacklist | └── XXX.merged.bed ├── variants | ├── XXX.all.vcf.gz | └── XXX.all.vcf.gz.tbi ├── sequences | ├── XXX.cdna.fasta | ├── XXX.cdna.fasta.fai | ├── XXX.dna.dict | ├── XXX.dna.fasta | └── XXX.dna.fasta.fai └── annotation ├── XXX.id_to_gene.tsv ├── XXX.t2g.tsv └── XXX.gtf
Extension | Content |
---|---|
.bed | Genome blacklisted regions |
.gtf | Genome annotation |
.id_to_gene.tsv | Genome id-to-name |
.t2g.tsv | Transcript id-to-name |
.fasta | Genome sequences |
.fasta.fai | Genome sequences index |
.dict | Genome sequences dictionary |
.vcf.gz | Genome known variations |
These files are quite volumous and are not embeded in this HTML page. Please find them directly on file system.