From e0a02de849c0db1f2137ddfde3f8c25dc7cf3bfb Mon Sep 17 00:00:00 2001 From: Emilio Palumbo Date: Fri, 2 Nov 2018 12:10:36 +0100 Subject: [PATCH] Add RNA-seq stats in README --- README.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7f59fc1..9e44803 100644 --- a/README.md +++ b/README.md @@ -36,13 +36,28 @@ The above metrics are computed for continuous and split mapped reads. An aggrega The `--uniq` (or `-u`) command line flag allows reporting of genome coverage statistics for uniquely mapped reads too. +## RNA-seq statistics + +The RNA-seq statistics follow [IHEC reccomendations for RNA-seq data quality metrics](https://github.com/IHEC/ihec-assay-standards/blob/199ec96b668114a90e39d3351358996287950dd1/qc_metrics/rna-seq/metrics.pdf). They include counts for the following regions: + +- intergenic (different from [coverage stats](#genome-coverage-statistics)) +- ribosomal RNA (`rRNA`) + +As long as other fractional metrics for the following read types: + +- mapped +- intergenic +- rRNA +- duplicates + ## Output examples: Some examples of the program output can be found in the `data` folder within the GitHub repository: - [General Stats](data/expected-general.json) - [Genomic coverage stats](data/expected-coverage.json) -- [Genomic coverage stats with uniquely mapped reads](data/expected-coverage-uniq.json) (Note that the `coverageUniq` stats are reported as an additional JSON object) +- [Genomic coverage stats with uniquely mapped reads](data/expected-coverage-uniq.json#L28) (Note that the `coverageUniq` stats are reported as an additional JSON object) +- [RNA-seq stats](data/expected-rnaseq.json#L51) ## License