results.rst

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/
├── XXX.all.vcf
├── XXX.cdna.fasta
├── XXX.cdna.fasta.fai
├── XXX.dna.dict
├── XXX.dna.fasta
├── XXX.dna.fasta.fai
├── XXX.tsv
└── XXX.gtf

Extension	Content
.gtf	Genome annotation
.tsv	Genome id-to-name
.fasta	Genome sequences
.fasta.fai	Genome sequences index
.dict	Genome sequences dictionary
.vcf	Genome known variations

These files are quite volumous and are not embeded in this HTML page. Please find them directly on file system.

Results

``` results/ ├── QC │   ├── MultiQC_FastQC_data.zip # Raw fastq file quality tables │   ├── MultiQC_FastQC.html # Raw fastq file quality report │   └── report_pe │   ├── YYY_fastqc.zip # Per-sample quality table │   └── YYY.html # Per-sample quality report └── XXX

├── QC │   ├── Mitochodrial_ratio.png # Mitochodrial ratio across samples │   ├── MultiQC_Quantification_data.zip # Complete pipeline statistics as TSV │   ├── MultiQC_Quantification.html # Quantification quality report │   ├── rRNA_ratio.png # rRNA ratio across samples │   └── Stats.csv.gz # (pseudo-)mapping statitstics └── Quantification

├── html_reports/ # View counts in your web-browser ├── Raw.genes.tsv # Raw gene abundance estimation ├── Raw.transcripts.tsv # Raw transcripts abundance estimation ├── TPM.genes.tsv # Normalized gene counts └── TPM.transcripts.tsv # Normalized transcripts counts

```