Output File Organization
The output files are organized into individual sample folders, group comparison folders, and the Global Analysis folder.
|
Folder |
Files |
Description |
|---|---|---|
|
Individual Sample folders |
BAM |
|
|
bai |
|
|
|
baseCoverage.csv |
Contains the number of bases aligned to each target. |
|
|
counts.txt |
Contains the number of read pairs aligned to each target. |
|
|
coverage.csv |
Contains the number of reads aligned to each target. |
|
|
exonvariants.csv |
See Exon Variant File Format for more information. |
|
|
exonvariants.vcf.gz |
See Exon Variant File Format for more information. |
|
|
fusions.csv |
See fusions.csv for more information. |
|
|
fusions.vcf.gz |
See fusions.vcf.gz for more information. |
|
|
putative.fusions.csv |
See putativefusions.csv for more information. |
|
|
report.html |
HTML version of the sample report. |
|
|
report.csv |
CSV version of the sample report. |
|
|
summary.csv |
Contains metrics for the sample. See Sample Summary Report for more information. |
|
|
Group Comparison folders |
deseq.counts.csv |
Contains raw counts of the compared samples |
|
deseq.disp.pdf |
Dispersion part generated by DESeq2. |
|
|
deseq.ma.pdf |
MA plot generated by DESeq2. |
|
|
deseq.metrics.csv |
Contains differential expression analysis metrics. |
|
|
deseq.res.csv |
Contains DESeq2 results. |
|
|
deseq.rlog.csv |
Contains regularized log-transformed counts calculated by DESeq2. |
|
|
Global Analysis folder |
TargetHitsPerSample_M1.tsv |
Contains the raw aligned replicate counts for each transcript. See Target Hits File Format for more information. |
|
TargetedRNASeqGeneExpression_M1.tsv |
See Gene Expression File Format for more information. |
|
|
aggregate.summary.csv |
Contains metrics for all the samples in the analysis. See Aggregate Summary Report for more information. |
|
|
deseq.corr.csv |
Pearson correlation between all the samples in the analysis calculated on log2-tranformed raw counts. |
|
|
deseq.corr.png |
Plot of sample correlation heatmap and dendrogram based on deseq.corr.csv. |
|
|
genes.cpm.csv |
Contains counts per million (CPM)-mapped reads normalized for library size across all the samples in the analysis. |
|
|
pca.csv |
Contains principal component analysis results. |
|
|
pca.png |
PCA plot based on the first two principal components that explain the most variance. |