diff --git a/README.md b/README.md index 5ecdc34..4838372 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,11 @@ together. The workflow also produces separate per-sample transcriptomes, so each sample has its own GTF, FASTA, count tables, and optional `SQANTI3` summary alongside the shared results. +
+wf-transcriptomes overview schematic. +
Schematic depicting wf-transcriptomes workflow.
+
+ For users familiar with earlier transcriptome workflows, the main change is that transcript discovery, quantification, and optional differential analysis now use the shared `bambu` outputs rather than the older diff --git a/docs/02_introduction.md b/docs/02_introduction.md index 72c427c..01ed80b 100644 --- a/docs/02_introduction.md +++ b/docs/02_introduction.md @@ -21,6 +21,11 @@ together. The workflow also produces separate per-sample transcriptomes, so each sample has its own GTF, FASTA, count tables, and optional `SQANTI3` summary alongside the shared results. +
+wf-transcriptomes overview schematic. +
Schematic depicting wf-transcriptomes workflow.
+
+ For users familiar with earlier transcriptome workflows, the main change is that transcript discovery, quantification, and optional differential analysis now use the shared `bambu` outputs rather than the older diff --git a/docs/images/wf-transcriptomes.drawio.svg b/docs/images/wf-transcriptomes.drawio.svg new file mode 100644 index 0000000..341ed6a --- /dev/null +++ b/docs/images/wf-transcriptomes.drawio.svg @@ -0,0 +1,4 @@ + + + +
Transcriptome construction
Differential expression
(Requires multiple conditions & replicates)
Sample Sheet
Reference Genome
Reference Annotation
Alignment Statistics
Transcriptome GTF
Annotation Summary
Classification Summary
DE Results
DTU Results
Transcriptome FASTA
Report HTML
Read Statistics
Transcriptome FASTA
Gene & Transcript Count TSVs
Classification Summary
Transcriptome GTF
Gene & Transcript Count TSVs
FASTQ
BAM
DEXSeq
Report
DESeq2
minimap2
bambu
fastcat
Prepare annotation
SQANTI3
Validation
wf-transcriptomes
v2.0.*
Main workflow
Per-sample analysis
Optional
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