bcbio-nextgen runs in a temporary work directory which contains a number of processing intermediates. Pipeline completion extracts the final useful output files into a separate directory, specified by the Upload. This configuration allows upload to local directories, Galaxy, or Amazon S3. Once extracting and confirming the output files, you can delete the temporary directory to save space.
The output directory contains sample specific output files labeled by sample name and a more general project directory. The sample directories contain all of the sample specific output files, while the project directory contains global files like project summaries or batched population level variant calls. See the Teaching documentation for a full variant calling example with additional details about configuration setting and resulting output files.
project-summary.yaml– Top level YAML format summary file with statistics on read alignments and duplications as well as analysis specific metrics.
programs.txt– Program versions for bcbio-nextgen and software run in the pipeline. This enables reproduction of analyses.
multiqcrun MultiQC to gather all QC metrics from different tools, such as, cutadapt, featureCounts, samtools, STAR … into an unique HTML report.
SAMPLE/qc– Directory of quality control runs for the sample. These include charts and metrics for assessing quality of sequencing and analysis.
SAMPLE-ready.bam– A prepared BAM file of the aligned reads. Depending on the analysis used, this may include trimmed, recalibrated and realigned reads following alignment.
grading-summary.csv– Grading details comparing each sample to a reference set of calls. This will only have information when providing a validation callset.
BATCH-caller.vcf– Variants called for a population/batch of samples by a particular caller.
BATCH-caller.db– A GEMINI database associating variant calls with a wide variety of third party annotations. This provides a queryable framework for assessing variant quality statistics.
SAMPLE-caller.vcf– Variants calls for an individual sample.
annotated_combined.counts– featureCounts counts matrix with gene symbol as an extra column.
combined.counts– featureCounts counts matrix with gene symbol as an extra column.
combined.dexseq– DEXseq counts matrix with exonID as first column.
combined.gene.sf.tmp– Sailfish gene count matrix normalized to TPM.
combined.isoform.sf.tpm– Sailfish transcript count matix normalized to TPM.
combined.sf– Sailfish raw output, all samples files are pasted one after another.
tx2gene.csv– Annotation file needed for DESeq2 to use Sailfish output.
SAMPLE-transcriptome.bam– BAM file aligned to transcriptome.
SAMPLE-ready.counts– featureCounts gene counts output.
sailfish– Sailfish output.
counts_mirna.tsv– miRBase miRNA count matrix.
counts.tsv– miRBase isomiRs count matrix.
counts_mirna_novel.tsv– miRDeep2 miRNA count matrix.
counts_novel.tsv– miRDeep2 isomiRs count matrix.
seqcluster– output of seqcluster tool. Inside this folder, counts.tsv has count matrix for all clusters found over the genome.
seqclusterViz– input file for interactive browser at https://github.com/lpantano/seqclusterViz
report– Rmd template to help with downstream analysis like QC metrics, differential expression, and clustering.
This section collects useful scripts and tools to do downstream analysis of bcbio-nextgen outputs. If you have pointers to useful tools, please add them to the documentation.