Inspect the reads
Review per-base quality, adapter content, duplication, sequence composition and GC and read-length distributions.
Read quality before interpretation.
FastQC in Bridge Horizon
FastQC checks sequencing reads before you rely on the analysis built from them. In Bridge Horizon, the Quality Control pipeline runs it on both reads of each sample and keeps the findings connected to the results that follow.
From reads to review
Input
Raw FASTQ reads, Read 1 and Read 2
Check
FastQC checks each read
Review
Per-read quality reports and experiment-level review
In your workflow
Know what went into your analysis
Read-level warnings are starting points for investigation, not automatic pass or fail decisions.
Compare before and after trimming
In the bulk RNA-seq pipeline, FastQC checks raw and trimmed reads so you can see what trimming changed and what concerns remain.
Make QC easier to discuss
Results appear with the run, and relevant FastQC metrics are included in the experiment's MultiQC report for cross-sample review.
Where FastQC appears
Quality Control
Every raw FASTQ sample receives a documented FastQC check. Some assay types also receive additional, assay-specific checks.
Explore pipelineBulk RNA-seq
Check both raw and trimmed reads before interpreting alignment and expression results.
Explore pipelineBulk TCR Detection
Check both reads before interpreting reconstructed receptors and clonotypes.
Explore pipelineReading the results
FastQC reports signals about read quality, not a verdict on whether a sample is usable. Interpret warnings in the context of the assay and downstream results.
Also see MultiQC in Bridge Horizon.
See it in action
See FastQC in your workflow
Talk through your assay, sample volume and reporting needs with our team.