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/ ├── 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