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Merge branch 'master' of github.com:paulstothard/helpful_commands
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paulstothard committed Oct 30, 2023
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Expand Up @@ -98,7 +98,7 @@ Command-line tools, commands, and code snippets for performing routine data proc
- [Kill all running containers](#kill-all-running-containers)
- [Delete all containers that are not running](#delete-all-containers-that-are-not-running)
- [Delete all images](#delete-all-images)
- [FASTA files](#fasta-files)
- [FASTA and FASTQ files](#fasta-and-fastq-files)
- [Split a multi-FASTA file into separate files named according to the sequence title](#split-a-multi-fasta-file-into-separate-files-named-according-to-the-sequence-title)
- [Download a reference genome FASTA file from Ensembl](#download-a-reference-genome-fasta-file-from-ensembl)
- [Download reference genome FASTA file and related files from NCBI](#download-reference-genome-fasta-file-and-related-files-from-ncbi)
Expand All @@ -108,6 +108,15 @@ Command-line tools, commands, and code snippets for performing routine data proc
- [Extract FASTA sequences from a file based on a file of sequence names of interest](#extract-fasta-sequences-from-a-file-based-on-a-file-of-sequence-names-of-interest)
- [Add a FASTA title to the start of a sequence in RAW format](#add-a-fasta-title-to-the-start-of-a-sequence-in-raw-format)
- [Reorder the sequences in a FASTA file based on a VCF file header](#reorder-the-sequences-in-a-fasta-file-based-on-a-vcf-file-header)
- [Download FASTQ files based on a list of SRA accessions using the SRA Toolkit](#download-fastq-files-based-on-a-list-of-sra-accessions-using-the-sra-toolkit)
- [Download FASTQ files based on a list of SRA accessions using Kingfisher](#download-fastq-files-based-on-a-list-of-sra-accessions-using-kingfisher)
- [Process FASTQ files in pairs](#process-fastq-files-in-pairs)
- [Count the bases in a FASTQ file](#count-the-bases-in-a-fastq-file)
- [Count the reads in a FASTQ file](#count-the-reads-in-a-fastq-file)
- [Merge compressed FASTQ files](#merge-compressed-fastq-files)
- [Process FASTQ files in pairs using parallel](#process-fastq-files-in-pairs-using-parallel)
- [Count reads in compressed FASTQ files using Slurm and parallel](#count-reads-in-compressed-fastq-files-using-slurm-and-parallel)
- [Run FastQC on compressed FASTQ files using Slurm and a job array](#run-fastqc-on-compressed-fastq-files-using-slurm-and-a-job-array)
- [File conversion](#file-conversion)
- [Convert CSV to TSV](#convert-csv-to-tsv)
- [Convert TSV to CSV](#convert-tsv-to-csv)
Expand Down Expand Up @@ -138,16 +147,13 @@ Command-line tools, commands, and code snippets for performing routine data proc
- [Download a GenBank file with curl](#download-a-genbank-file-with-curl)
- [Download sequences from the NCBI Assembly database](#download-sequences-from-the-ncbi-assembly-database)
- [Download reference genomes and related files from NCBI](#download-reference-genomes-and-related-files-from-ncbi)
- [Download fastq files based on a list of SRA accessions using the SRA Toolkit](#download-fastq-files-based-on-a-list-of-sra-accessions-using-the-sra-toolkit)
- [Download fastq files based on a list of SRA accessions using Kingfisher](#download-fastq-files-based-on-a-list-of-sra-accessions-using-kingfisher)
- [Download a reference genome GTF file from Ensembl](#download-a-reference-genome-gtf-file-from-ensembl)
- [Download files from a Globus endpoint using Globus CLI](#download-files-from-a-globus-endpoint-using-globus-cli)
- [find](#find)
- [Perform a series of commands on files returned by find](#perform-a-series-of-commands-on-files-returned-by-find)
- [Sort files by name before processing](#sort-files-by-name-before-processing)
- [Sort the files by creation time before processing](#sort-the-files-by-creation-time-before-processing)
- [Use files as the argument list for a command](#use-files-as-the-argument-list-for-a-command)
- [Process files in pairs](#process-files-in-pairs)
- [Copy the files returned by find](#copy-the-files-returned-by-find)
- [Copy the files returned by find, naming the copies after a directory in the path](#copy-the-files-returned-by-find-naming-the-copies-after-a-directory-in-the-path)
- [Switch to the directory containing each file and execute a command](#switch-to-the-directory-containing-each-file-and-execute-a-command)
Expand Down Expand Up @@ -234,19 +240,15 @@ Command-line tools, commands, and code snippets for performing routine data proc
- [Perform a calculation using expr](#perform-a-calculation-using-expr)
- [Performa a calculation using qalc](#performa-a-calculation-using-qalc)
- [Perform a remote BLAST search](#perform-a-remote-blast-search)
- [Count the bases in a fastq file](#count-the-bases-in-a-fastq-file)
- [Count the reads in a fastq file](#count-the-reads-in-a-fastq-file)
- [Use SQL-like queries to work with a CSV or TSV file](#use-sql-like-queries-to-work-with-a-csv-or-tsv-file)
- [Browse, search, and edit a large CSV file](#browse-search-and-edit-a-large-csv-file)
- [Prevent a command from stopping when you log out or exit the shell](#prevent-a-command-from-stopping-when-you-log-out-or-exit-the-shell)
- [Edit a PDF file](#edit-a-pdf-file)
- [Merge compressed fastq files](#merge-compressed-fastq-files)
- [Calculate coverage statistics for a BAM file](#calculate-coverage-statistics-for-a-bam-file)
- [Reverse the order of lines in a file](#reverse-the-order-of-lines-in-a-file)
- [parallel](#parallel)
- [Extract files in parallel](#extract-files-in-parallel)
- [Compress files in parallel](#compress-files-in-parallel)
- [Process files in pairs using parallel](#process-files-in-pairs-using-parallel)
- [Perform BLAST in parallel](#perform-blast-in-parallel)
- [Read parameters from a file using parallel](#read-parameters-from-a-file-using-parallel)
- [Perform a separate BLAST search for each query and database using parallel](#perform-a-separate-blast-search-for-each-query-and-database-using-parallel)
Expand Down Expand Up @@ -296,8 +298,6 @@ Command-line tools, commands, and code snippets for performing routine data proc
- [Delete lines](#delete-lines)
- [Share data with project group members](#share-data-with-project-group-members)
- [Slurm](#slurm)
- [Count reads in compressed fastq files](#count-reads-in-compressed-fastq-files)
- [Run fastqc on compressed fastq files using a job array](#run-fastqc-on-compressed-fastq-files-using-a-job-array)
- [Merge VCF files in batches](#merge-vcf-files-in-batches)
- [Merge VCF files in batches using a job array](#merge-vcf-files-in-batches-using-a-job-array)
- [Run a Snakemake workflow](#run-a-snakemake-workflow)
Expand Down

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