From 361ec74046d752d9530f51b46a27b05650488d0d Mon Sep 17 00:00:00 2001 From: Joyjit Daw Date: Wed, 3 Apr 2024 13:09:29 -0400 Subject: [PATCH] patch up README --- README.md | 2 +- documentation/CustomBarcodes.md | 2 +- documentation/PolyTailConfig.md | 50 --------------------------------- 3 files changed, 2 insertions(+), 52 deletions(-) delete mode 100644 documentation/PolyTailConfig.md diff --git a/README.md b/README.md index 3e4fd5e24..57d534909 100644 --- a/README.md +++ b/README.md @@ -278,7 +278,7 @@ In addition to supporting the standard barcode kits from Oxford Nanopore, Dorado ### Poly(A) tail estimation -Dorado has initial support for estimating poly(A) tail lengths for cDNA (PCS and PCB kits) and RNA. Note that Oxford Nanopore cDNA reads are sequenced in two different orientations and Dorado poly(A) tail length estimation handles both (A and T homopolymers). This feature can be enabled by passing `--estimate-poly-a` to the `basecaller` command. It is disabled by default. The estimated tail length is stored in the `pt:i` tag of the output record. Reads for which the tail length could not be estimated will not have the `pt:i` tag. Custom primer sequences and estimation of interrupted tails can be configured through the `--poly-a-config` option. See [here](documentation/PolyTailConfig.md) for more details. +Dorado has initial support for estimating poly(A) tail lengths for cDNA (PCS and PCB kits) and RNA. Note that Oxford Nanopore cDNA reads are sequenced in two different orientations and Dorado poly(A) tail length estimation handles both (A and T homopolymers). This feature can be enabled by passing `--estimate-poly-a` to the `basecaller` command. It is disabled by default. The estimated tail length is stored in the `pt:i` tag of the output record. Reads for which the tail length could not be estimated will not have the `pt:i` tag. Note that if this option is used, then adapter/primer/barcode trimming will be automatically **disabled** for DNA. diff --git a/documentation/CustomBarcodes.md b/documentation/CustomBarcodes.md index add33f5a8..5487a5833 100644 --- a/documentation/CustomBarcodes.md +++ b/documentation/CustomBarcodes.md @@ -17,7 +17,7 @@ A double-ended barcode with different flanks and barcode sequences for front and ## Specification Format -The custom arrangements are defined using a `toml` file, and custom barcode sequences are passed through a `FASTQ` file. +The custom arrangements are defined using a `toml` file, and custom barcode sequences are passed through a `FASTA` file. ### Arrangement File diff --git a/documentation/PolyTailConfig.md b/documentation/PolyTailConfig.md deleted file mode 100644 index dc66f56a5..000000000 --- a/documentation/PolyTailConfig.md +++ /dev/null @@ -1,50 +0,0 @@ -# Custom Poly Tail Configuration - -Dorado supports estimation of Poly(A/T) tails for DNA (PCS AND PCB) and RNA samples. The default settings are optimized for non-interrupted Poly(A/T) sequences that occur at read ends. - -Dorado also supports additional features that can be customized through a configuration file (described below): -* Custom primer sequence for cDNA tail estimation -* Clustering of interrupted Poly(A/T) tails - -## Poly(A/T) Reference Diagram - -``` -cDNA - -5' ---- ADAPTER ---- FRONT_PRIMER ---- cDNA ---- poly(A) ---- RC(REAR_PRIMER) ---- 3' - -OR - -5' ---- ADAPTER ---- REAR_PRIMER ---- poly(T) ---- RC(cDNA) ---- RC(FRONT_PRIMER) ---- 3' -``` - -``` -dRNA - -3' ---- ADAPTER ---- poly(A) ---- RNA ---- 5' -``` - -## Configuration Format - -The configuration file needs to be in the `toml` format. - -``` -[anchors] -front_primer = "ATCG" -rear_primer = "CGTA" - -[threshold] -flank_threshold = 10 - -[tail] -tail_interrupt_length = 10 -``` - -### Configuration Options - -| Option | Description | -| -- | -- | -| front_primer | Front primer sequence for cDNA | -| rear_primer | Rear primer sequence for cDNA | -| flank_threshold | The edit distance threshold to use for detection of the flank/primer sequences | -| tail_interrupt_length | Combine tails that are within this distance of each other (default is 0, i.e. don't combine any) |