results.rst

Results

Alongside with the report, you may find directories called reference, and results.

Results files list

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

Reference

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.