### Build Mudskipper from Source Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Builds the Mudskipper project in release mode using Cargo. Ensure you have the Rust toolchain installed with a minimum rustc version of 1.51.0. ```bash cargo build --release ``` -------------------------------- ### Mudskipper sc Options Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Lists available options for the 'mudskipper sc' command, including required and optional arguments for input files, output formats, and processing parameters. ```bash OPTIONS: -a, --alignment Input SAM/BAM file -g, --gtf Input GTF/GFF file -i, --index Index directory containing parsed GTF files -o, --out Output file name (or directory name when --rad is passed) -s, --max-softclip Max allowed softclip length [default: 50] -t, --threads Number of threads for processing bam files [default: 1] -r, --rad Output in RAD format instead of BAM -m, --rad-mapped The name of output rad file; Only used with --rad [default: map.rad] -u, --rad-unmapped The name of file containing the number of unmapped reads for each barcode; Only used with --rad [default: unmapped_bc_count.bin] -c, --corrected-tags Output error-corrected cell barcode and UMI -h, --help Prints help information -V, --version Prints version information ``` -------------------------------- ### Build and Store GTF Interval Tree Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Use this command to build an interval tree from a GTF file and store it in a specified directory. This is useful for reusing the index across multiple analyses. ```bash mudskipper index --gtf --dir-index ``` -------------------------------- ### Build and Store GTF Index Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Build and store a GTF index for efficient repeated use. This is beneficial if you plan to convert multiple BAM/SAM files using the same annotation. ```bash # build and store a GTF index; useful if you want to convert multiple BAM/SAM files mudkipper index --gtf annotation.gtf --dir-index gtf_index ``` -------------------------------- ### Run Mudskipper with Pre-built GTF Index Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Execute mudskipper using a pre-built GTF index for faster processing. This applies to both bulk and single-cell RNA-Seq conversions. ```bash # run mudskipper using the pre-built GTF index mudkipper bulk --index gtf_index --alignment genomic.bam --out transcriptomic.bam mudkipper sc --index gtf_index --alignment genomic.sam --out transcriptomic_dir ``` -------------------------------- ### Project Bulk RNA-Seq Read Alignments Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Projects bulk RNA-Seq read alignments using the `mudskipper bulk` command. Requires input alignment and either a GTF file or a pre-built index, and an output file path. Supports various options for filtering and output format. ```bash mudskipper bulk [OPTIONS] --alignment (--gtf |--index ) --out ``` -------------------------------- ### Mudskipper sc Command Usage Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Basic command structure for projecting single-cell RNA-Seq read alignments. Requires alignment file and either GTF or index. Output file/directory is mandatory. ```bash mudskipper sc [OPTIONS] --alignment (--gtf |--index ) --out ``` -------------------------------- ### Convert Bulk RNA-Seq Genomic BAM to Transcriptomic BAM Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Use this command to convert a bulk RNA-Seq genomic BAM file to a transcriptomic BAM file, suitable for quantification with Salmon. Ensure you have the GTF annotation file. ```bash # convert a bulk RNA-Seq genomic BAM to a transcriptomic BAM for quantification with Salmon mudkipper bulk --gtf annotation.gtf --alignment genomic.bam --out transcriptomic.bam ``` -------------------------------- ### Convert Single-Cell RNA-Seq Genomic SAM to Transcriptomic RAD Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md This command converts a single-cell RNA-Seq genomic SAM file to a transcriptomic RAD directory for quantification with alevin-fry. Provide the GTF annotation file and the genomic SAM alignment. ```bash # convert a single-cell RNA-Seq genomic SAM to a transcriptomic RAD for quantification with alevin-fry mudkipper sc --gtf annotation.gtf --alignment genomic.sam --out transcriptomic_dir ``` -------------------------------- ### Add Mudskipper to PATH Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Temporarily adds the directory containing the Mudskipper executable to your system's PATH environment variable for convenient access. ```bash export PATH=`pwd`/target/release/:$PATH ``` -------------------------------- ### Projection of bulk RNA-Seq read alignments Source: https://github.com/oceangenomics/mudskipper/blob/main/README.md Projects bulk RNA-Seq read alignments against a reference genome using either a GTF file or a pre-built index. It supports various output formats and configuration options. ```APIDOC ## mudskipper bulk ### Description Projects bulk RNA-Seq read alignments against a reference genome using either a GTF file or a pre-built index. It supports various output formats and configuration options. ### Method CLI Command ### Endpoint mudskipper bulk [OPTIONS] ### Parameters #### Required arguments - **--alignment ** (FILE) - Required - Input SAM/BAM file. This BAM/SAM file should contain alignment of short RNA-Seq reads against reference genome. The alignments stored in this file are potentially spliced. - **--gtf ** (FILE) - Required - Input GTF/GFF file. The interval tree is built from the GTF file on the fly. Make sure that the GTF file corresponds to the same version of the reference genome to which short reads have been aligned. If some target sequences are missing from the GTF file, alignments to those target sequences will be dropped automatically. - **--index ** (DIR) - Required - Index directory containing parsed GTF files. This is helpful if you wish to run `mudskipper` on many BAM/SAM files. Note that `--gtf` and `--index` are mutually exclusive. - **--out ** (FILE) - Required - Output file name. By default, the output alignment file is in BAM format. If `--rad` is passed, then the output alignment file will be in RAD format. #### Optional arguments - **--max-softclip ** (INT) - Optional - Max allowed softclip length [default: 50] - **--threads ** (INT) - Optional - Number of threads for processing bam files [default: 1] - **--rad** - Optional - Output in RAD format instead of BAM. - **--help** - Optional - Prints help information - **--version** - Optional - Prints version information ``` === COMPLETE CONTENT === This response contains all available snippets from this library. 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