From 94ce1162a8230048159f428cda255287c85b1ce9 Mon Sep 17 00:00:00 2001 From: pdimens Date: Wed, 11 Dec 2024 13:42:47 -0500 Subject: [PATCH] make own page --- Workflows/downsample.md | 69 +++++++++++++++++++++++++++++++++++++++++ Workflows/other.md | 41 ------------------------ 2 files changed, 69 insertions(+), 41 deletions(-) create mode 100644 Workflows/downsample.md diff --git a/Workflows/downsample.md b/Workflows/downsample.md new file mode 100644 index 00000000..ebf397e3 --- /dev/null +++ b/Workflows/downsample.md @@ -0,0 +1,69 @@ +--- +label: Downsample +description: Downsample data by barcode +icon: fold-down +order: 10 +--- + +# :icon-fold-down: Downsample data by barcode + +=== :icon-checklist: You will need one of either +- one alignment file [!badge variant="success" text=".bam"] [!badge variant="success" text=".sam"] [!badge variant="secondary" text="case insensitive"] +- one set of paired-end reads in FASTQ format [!badge variant="success" text=".fq"] [!badge variant="success" text=".fastq"] [!badge variant="secondary" text="gzip recommended"] [!badge variant="secondary" text="case insensitive"] +=== + +While downsampling (subsampling) FASTQ and BAM files is relatively simple with tools such as `awk`, `samtools`, `seqtk`, `seqkit`, etc., +[!badge corners="pill" text="downsample"] allows you to downsample a BAM file (or paired-end FASTQ) _by barcodes_. That means you can +keep all the reads associated with `d` number of barcodes. The `--invalid` proportion will determine what proportion of invalid barcodes appear in the barcode +pool that gets subsampled, where `0` is none, `1` is all invalid barcodes, and a number in between is that proportion, e.g. `0.5` is half. +Bear in mind that the barcode pool still gets subsampled, so the `--invalid` proportion doesn't necessarily reflect how many end up getting +sampled, rather what proportion will be considered for sampling. + +!!! Barcode tag +Barcodes must be in the `BX:Z` SAM tag for both BAM and FASTQ inputs. See [Section 1 of the SAM Spec here](https://samtools.github.io/hts-specs/SAMtags.pdf). +!!! + +```bash usage +harpy downsample OPTIONS... INPUT(S)... +``` + +```bash example +# BAM file +harpy downsample -d 1000 -i 0.3 -p sample1.sub1000 sample1.bam + +# FASTQ file +harpy downsample -d 1000 -i 0 -p sample1.sub1000 sample1.F.fq.gz sample1.R.fq.gz +``` + +## :icon-terminal: Running Options +In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="downsample"] +module is configured using the command-line arguments below. + +{.compact} +| argument | short name | default | description | +| :-------------- | :--------: | :-----------: | :-------------------------------------------------------------------------------------------------------------------------------- | +| `INPUT(S)` | | | [!badge variant="info" text="required"] One BAM file or both read files from a paired-end FASTQ pair | +| `--downsample` | `-d` | | [!badge variant="info" text="required"] Number of barcodes to downsample to | +| `--invalid` | `-i` | `1` | Proportion of barcodes to sample | +| `--prefix` | `-p` | `downsampled` | Prefix for output files | +| `--random-seed` | | | Random seed for sampling [!badge variant="secondary" text="optional"] | + +---- +## :icon-git-pull-request: Downsample Workflow +```mermaid +graph LR + subgraph fastq + R1([read 1]):::clean---R2([read 2]):::clean + end + subgraph bam + bamfile([bam]):::clean + end + fastq-->|bam conversion|bam + bam-->sub([extract and\n subsample barcodes]):::clean + sub-->exreads([extract reads]):::clean + bam-->exreads + fastq-->exreads + style fastq fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px + style bam fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px + classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px +``` \ No newline at end of file diff --git a/Workflows/other.md b/Workflows/other.md index a25528fa..aa1106fb 100644 --- a/Workflows/other.md +++ b/Workflows/other.md @@ -11,7 +11,6 @@ On this page you'll find Harpy functions that do other, ancillary things. {.compact} | module | description | | :------------- | :------------------------------------------------------------------------------- | -| `downsample` | Downsample BAM or FASTQ files by barcode | | `imputeparams` | Create a template imputation parameter file | | `resume` | Continue a Harpy workflow from an existing output folder | | `popgroup` | Create generic sample-group file using existing sample file names (fq.gz or bam) | @@ -19,46 +18,6 @@ On this page you'll find Harpy functions that do other, ancillary things. --- -### downsample -While downsampling (subsampling) FASTQ and BAM files is relatively simple with tools such as `awk`, `samtools`, `seqtk`, `seqkit`, etc., -Harpy offers the `downsample` module, which allows you to downsample a BAM file (or paired-end FASTQ) _by barcodes_. That means you can -keep all the reads associated with `d` number of barcodes. First, barcodes are extracted, then subsampled, then the reads associated -with those barcodes are extracted. The `--invalid` proportion will determine what proportion of invalid barcodes appear in the barcode -pool that gets subsampled, where `0` is none, `1` is all invalid barcodes, and a number in between is that proportion, e.g. `0.5` is half. -Bear in mind that the barcode pool still gets subsampled, so the `--invalid` proportion doesn't necessarily reflect how many end up getting -sampled, rather what proportion will be considered for sampling. - -!!! Barcode tag -Barcodes must be in the `BX:Z` SAM tag for both BAM and FASTQ inputs. See [Section 1 of the SAM Spec here](https://samtools.github.io/hts-specs/SAMtags.pdf). -!!! - -```bash usage -harpy downsample OPTIONS... INPUT(S)... -``` - -```bash example -# BAM file -harpy downsample -d 1000 -i 0.3 -p sample1.sub1000 sample1.bam - -# FASTQ file -harpy downsample -d 1000 -i 0 -p sample1.sub1000 sample1.F.fq.gz sample1.R.fq.gz -``` - -#### arguments -{.compact} -| argument | short name | default | description | -| :-------------- | :--------: | :-----------: | :-------------------------------------------------------------------------------------------------------------------------------- | -| `INPUT(S)` | | | [!badge variant="info" text="required"] One BAM file or both read files from a paired-end FASTQ pair | -| `--downsample` | `-d` | | [!badge variant="info" text="required"] Number of barcodes to downsample to | -| `--invalid` | `-i` | 1 | Proportion of barcodes to sample | -| `--prefix` | `-p` | `downsampled` | Prefix for output files | -| `--random-seed` | | | Random seed for sampling [!badge variant="secondary" text="optional"] | -| `--snakemake` | | | Additional Snakemake arguments, in quotes | -| `--threads` | `-t` | `4` | Number of threads to use | -| `--quiet` | | | Don't show output text while running | - ---- - ### imputeparams Create a template parameter file for the [!badge corners="pill" text="impute"](/Workflows/impute.md) module. The file is formatted correctly and serves as a starting point for using parameters that make sense for your study.