From 88bb8ffe8f37d9332a78145c482b7112a82761d0 Mon Sep 17 00:00:00 2001 From: Jessica Mattick Date: Fri, 8 Dec 2023 10:36:45 -0600 Subject: [PATCH] Update min-score and hifi presets docs --- docs/faq/filter-input.md | 2 +- docs/faq/hifi-presets.md | 12 ++++-------- 2 files changed, 5 insertions(+), 9 deletions(-) diff --git a/docs/faq/filter-input.md b/docs/faq/filter-input.md index dd10ce1..674e60b 100644 --- a/docs/faq/filter-input.md +++ b/docs/faq/filter-input.md @@ -14,7 +14,7 @@ step. The default is `0`, meaning deactivated. ## `--min-score` Threshold for the average barcode score of the leading and trailing ends. -ZMWs with barcode score below `N` are omitted. The default is `0`. +ZMWs with barcode score below or equal to `N` are omitted. The default is `0`. It is advised to set it to `26` for CLR and `80` for HiFi. ## `--min-passes` diff --git a/docs/faq/hifi-presets.md b/docs/faq/hifi-presets.md index 9435a2e..780343a 100644 --- a/docs/faq/hifi-presets.md +++ b/docs/faq/hifi-presets.md @@ -6,17 +6,13 @@ title: HiFi Presets ## HiFi presets With v2.5.0 we introduced the concept of recommended parameter presets called -`--hifi-preset`. All preset use - - --ccs --min-score 80 --min-end-score 50 --min-ref-span 0.75 - -in addition they differ as following +`--hifi-preset`. | Preset | Definition | | -------------------- | ------------------------------------- | -| `SYMMETRIC` | `--same` | -| `SYMMETRIC-ADAPTERS` | `--same --ignore-missing-adapters` | -| `ASYMMETRIC` | `--different --min-scoring-regions 2` | +| `SYMMETRIC` | `--ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --single-end` | +| `SYMMETRIC-ADAPTERS` | `--ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --ignore-missing-adapters --single-end` | +| `ASYMMETRIC` | `--ccs --min-score 80 --min-end-score 50 --min-ref-span 0.75 --different --min-scoring-regions 2` | For barcoded adapter libraries, `SYMMETRIC-ADAPTERS` will increase demultiplexed yield. More info under [barcoded adapter FAQ](/faq/barcoded-adapter)