SmallRNA pipeline, file tools/fastq_stats/cutadapt_stats.R. In the plots "ProperlyTrimmed" is misleading in that it represents "trimmed reads" (Reads with adapters) rather than reads that pass the filter:
=== Summary ===
Total reads processed: 37,521,139
Reads with adapters: 37,315,087 (99.5%)
Reads that were too short: 5,698,454 (15.2%)
Reads that were too long: 15,139,760 (40.3%)
Reads written (passing filters): 16,682,925 (44.5%)
We should re-label it, and/or add a bar for "Reads written" which is an informative metric as well.
SmallRNA pipeline, file
tools/fastq_stats/cutadapt_stats.R. In the plots "ProperlyTrimmed" is misleading in that it represents "trimmed reads" (Reads with adapters) rather than reads that pass the filter:We should re-label it, and/or add a bar for "Reads written" which is an informative metric as well.