### Example YAML Parameters File for nf-core/nascent Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This YAML snippet provides an example structure for a params.yaml file. It shows how to define common pipeline parameters such as input samplesheet, output directory, and genome, which can then be loaded via the -params-file option. ```yaml input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' <...> ``` -------------------------------- ### Configure GroHMM Parameters Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md Example JSON configuration to specify fixed `grohmm_min_uts`, `grohmm_max_uts`, `grohmm_min_ltprobb`, and `grohmm_max_ltprobb` values for the GroHMM transcript identification method, bypassing the automatic parameter tuning process. ```JSON { "grohmm_min_uts": 15, "grohmm_max_uts": 15, "grohmm_min_ltprobb": -200, "grohmm_max_ltprobb": -200 } ``` -------------------------------- ### Full Samplesheet Example for nf-core/nascent (Single and Paired-End) Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This comprehensive CSV example demonstrates a samplesheet that includes both single-end and paired-end sequencing data. The nf-core/nascent pipeline is designed to auto-detect the read type based on the presence of the 'fastq_2' column. While additional columns can be included, the first three columns ('sample', 'fastq_1', 'fastq_2') are strictly mandatory for proper pipeline execution. ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, ``` -------------------------------- ### Samplesheet Example for Multiple Runs of Same Sample (nf-core/nascent) Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This CSV snippet illustrates how to structure a samplesheet when a single biological sample has been sequenced across multiple lanes or runs. By using the same 'sample' identifier, the pipeline will automatically concatenate the raw reads from all specified files before proceeding with downstream analysis. ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz ``` -------------------------------- ### Run nf-core/nascent Pipeline with Nextflow Source: https://github.com/nf-core/nascent/blob/main/README.md This command executes the nf-core/nascent pipeline using Nextflow. It specifies a profile for the execution environment (e.g., Docker, Singularity), the input samplesheet, and the output directory. Parameters should be provided via CLI or the -params-file option. ```bash nextflow run nf-core/nascent \\ -profile \\ --input samplesheet.csv \\ --outdir ``` -------------------------------- ### Prepare Samplesheet for nf-core/nascent Pipeline Source: https://github.com/nf-core/nascent/blob/main/README.md This CSV samplesheet defines the input data for the nf-core/nascent pipeline. Each row represents a fastq file (single-end) or a pair of fastq files (paired-end), specifying the sample name and paths to the corresponding FASTQ files. ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz ``` -------------------------------- ### Run nf-core/nascent Pipeline with Docker Profile Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This command illustrates the standard way to execute the nf-core/nascent pipeline. It specifies input data, an output directory, the target genome, and activates the 'docker' configuration profile for containerized execution. ```bash nextflow run nf-core/nascent --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` -------------------------------- ### Execute nf-core/nascent Pipeline Using a Parameters File Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This command demonstrates how to run the nf-core/nascent pipeline by loading all parameters from an external YAML or JSON file. This method is useful for managing complex or frequently reused parameter sets. ```bash nextflow run nf-core/nascent -profile docker -params-file params.yaml ``` -------------------------------- ### Samplesheet Column Definitions for nf-core/nascent Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This API documentation outlines the required columns for the nf-core/nascent pipeline samplesheet. It details the purpose and expected format for 'sample' identifiers, and paths to 'fastq_1' (read 1) and 'fastq_2' (read 2) files, which must be gzipped. ```APIDOC sample: description: Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (_). fastq_1: description: Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". fastq_2: description: Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". ``` -------------------------------- ### Configure Nextflow Compute Environment Profile Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md Describes the -profile argument for selecting configuration presets for different compute environments (Docker, Singularity, Conda, etc.). It explains how multiple profiles can be loaded and their loading order, with later profiles overwriting earlier ones. Using containers like Docker or Singularity is highly recommended for full reproducibility. ```APIDOC Command: -profile [,...] Description: Selects a configuration profile for the compute environment. Multiple profiles can be loaded in sequence, so later profiles can overwrite earlier profiles. If not specified, the pipeline runs locally expecting software on PATH (not recommended). Available Profiles: - test: A profile with a complete configuration for automated testing; includes links to test data. - docker: A generic configuration profile to be used with Docker. - singularity: A generic configuration profile to be used with Singularity. - podman: A generic configuration profile to be used with Podman. - shifter: A generic configuration profile to be used with Shifter. - charliecloud: A generic configuration profile to be used with Charliecloud. - apptainer: A generic configuration profile to be used with Apptainer. - wave: A generic configuration profile to enable Wave containers (requires Nextflow 24.03.0-edge or later); use together with one of the above. - conda: A generic configuration profile to be used with Conda (only as a last resort when containers are not possible). Example: -profile test,docker ``` -------------------------------- ### Understand nf-core/nascent Pipeline Output Structure Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This snippet outlines the key files and directories generated by the Nextflow pipeline in the working directory. It includes the work directory for intermediate files, the user-defined output directory, and Nextflow's log files. ```bash work # Directory containing the nextflow working files # Finished results in specified location (defined with --outdir) .nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` -------------------------------- ### Nextflow Pipeline Configuration Summary Generation Source: https://github.com/nf-core/nascent/blob/main/assets/email_template.html This snippet demonstrates the Groovy/Nextflow templating code responsible for iterating through a 'summary' map to display pipeline configuration key-value pairs in the report. It's designed to dynamically list all configured parameters. ```Nextflow <% out << summary.collect{ k,v -> "" }.join("\\n") %> $k $v ``` -------------------------------- ### MultiQC Report Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md Outlines the output files produced by MultiQC, including the main HTML report, parsed statistics, and static plots, summarizing QC results from various pipeline tools. ```APIDOC multiqc/ multiqc_report.html: a standalone HTML file that can be viewed in your web browser. multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline. multiqc_plots/: directory containing static images from the report in various formats. ``` -------------------------------- ### Specify Samplesheet Input Path for nf-core/nascent Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This command-line parameter is used to provide the path to the samplesheet file required by the nf-core/nascent pipeline. The samplesheet must be a comma-separated file containing at least three specific columns and a header row. ```bash --input '[path to samplesheet file]' ``` -------------------------------- ### fastp Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md fastp is a tool designed to provide fast, all-in-one preprocessing for FastQ files. It has been developed in C++ with multithreading support to achieve higher performance. fastp is used in this pipeline for standard adapter trimming and quality filtering. ```APIDOC - `preprocessing/fastp` - `*.fastp.html`: Trimming report in html format. - `*.fastp.json`: Trimming report in json format. - `*.fastp.log`: Trimming log file. ``` -------------------------------- ### Specify Pipeline Version for Reproducibility Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md Explains how to use the -r flag to specify a pipeline version, ensuring consistent execution and logging the version in reports. This helps in maintaining reproducibility across different runs. ```APIDOC Command: -r Description: Specifies the pipeline version for reproducible runs. This version is logged in reports (e.g., MultiQC). Example: -r 1.3.1 ``` -------------------------------- ### Nextflow Pipeline Launch Command Reference Source: https://github.com/nf-core/nascent/blob/main/assets/email_template.html This section of the report indicates where the exact command used to launch the Nextflow pipeline would be displayed. It serves as a record of the execution command, useful for reproducibility and auditing. ```Shell $commandLine ``` -------------------------------- ### deepTools bamcoverage Output Files for Coverage Graphs Source: https://github.com/nf-core/nascent/blob/main/docs/output.md deepTools bamcoverage generates sample coverage files in bigWig format, which are commonly used for visualizing sequencing coverage. These files provide strand-specific coverage (negative and positive strands) for downstream analysis and display. ```APIDOC coverage_graphs/: *.minus.bigWig: Sample coverage file (negative strand only) in bigWig format *.plus.bigWig: Sample coverage file (positive strand only) in bigWig format ``` -------------------------------- ### Specify Custom Nextflow Configuration File Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md Describes the -c argument, a core Nextflow command, for providing a path to a specific custom configuration file. This allows users to apply their own settings to the pipeline run. ```APIDOC Command: -c Description: Specifies the path to a specific custom Nextflow configuration file. Example: -c my_custom_config.config ``` -------------------------------- ### Resume Nextflow Pipeline Execution Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md Explains the -resume argument for restarting a pipeline, utilizing cached results from previous steps where the inputs are considered the same (identical names and file contents). It also mentions how to resume a specific run by name, which can be found using the 'nextflow log' command. ```APIDOC Command: -resume [run-name] Description: Restarts a pipeline, using cached results from any pipeline steps where the inputs are the same. For input to be considered the same, both names and file contents must be identical. Can also resume a specific run by providing its name. Usage: -resume -resume my_specific_run ``` -------------------------------- ### FastQC Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md FastQC gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the FastQC help pages. ```APIDOC - `preprocessing/fastqc` - `*_fastqc.html`: FastQC report containing quality metrics. - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. ``` -------------------------------- ### Nextflow Pipeline Information and Reports Source: https://github.com/nf-core/nascent/blob/main/docs/output.md Details the various reports and information files generated by Nextflow and the pipeline itself, including execution reports, timelines, traces, DAGs, and pipeline-specific reports like `pipeline_report.html` and `software_versions.yml`. ```APIDOC pipeline_info/ Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg. Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline. Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv. Parameters used by the pipeline run: params.json. ``` -------------------------------- ### BBMap Pileup Tool Output Files and Coverage Analysis Source: https://github.com/nf-core/nascent/blob/main/docs/output.md BBMap includes a `pileup` tool designed to analyze sequencing coverage for each sample. It generates detailed statistics and histograms of read coverage across chromosomes, providing insights into %GC content, positive/negative strand coverage, and total coverage. ```APIDOC quality_control/bbmap/: *.coverage.hist.txt: Histogram of read coverage over each chromosome *.coverage.stats.txt: Coverage stats broken down by chromosome including %GC, pos/neg read coverage, total coverage, etc. ``` -------------------------------- ### Preseq Tool Output Files and Functionality Source: https://github.com/nf-core/nascent/blob/main/docs/output.md Preseq is a tool for predicting and estimating the complexity of genomic sequencing libraries. It helps determine the utility of further sequencing by analyzing redundant reads and expected yields. The output files include extrapolated yield and cumulative coverage curves, along with command logs. ```APIDOC quality_control/preseq/: *.lc_extrap.txt: Preseq expected future yield file. *.c_curve.txt: Preseq cumulative coverage curve file. quality_control/preseq/log/: *.command.log: Standard error output from command. ``` -------------------------------- ### featureCounts Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md Details the output files generated by the featureCounts quantification tool, including biotype-level quantification results and summary statistics for both general and nascent transcripts. ```APIDOC quantification/featurecounts/ gene/*.featureCounts.txt: featureCounts biotype-level quantification results for each sample. gene/*.featureCounts.txt.summary: featureCounts summary file containing overall statistics about the counts. nascent/*.featureCounts.txt: featureCounts of nascent transcripts quantification results for each sample. nascent/*.featureCounts.txt.summary: featureCounts summary file of the nascent transcripts containing overall statistics about the counts. ``` -------------------------------- ### BWA-mem2 Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md BWA-mem2 is a software package for mapping low-divergent sequences against a large reference genome.The aligned reads are then coordinate-sorted with samtools. ```APIDOC - `bwamem2/` - `*.bam`: The original BAM file containing read alignments to the reference genome. ``` -------------------------------- ### Reference Genome Files Output Source: https://github.com/nf-core/nascent/blob/main/docs/output.md Describes the directory structure and files generated for reference genomes and indices (BWA, BWA-MEM2, DRAGMAP, Bowtie2) when the `--save_reference` parameter is used. ```APIDOC reference/ *.fa, *.gtf, *.gff, *.bed, .tsv: If the --save_reference parameter is provided then all of the genome reference files will be placed in this directory. bwa/: Directory containing bwa indices. bwa-mem2/: Directory containing bwa-mem2 indices. dragmap/: Directory containing DRAGMAP indices. bowtie2/: Directory containing bowtie2 indices. ``` -------------------------------- ### BWA Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md BWA is a software package for mapping low-divergent sequences against a large reference genome. The aligned reads are then coordinate-sorted is used for duplicate marking) with samtools. ```APIDOC - `bwa/` - `*.bam`: The original BAM file containing read alignments to the reference genome. ``` -------------------------------- ### HOMER Tool Output Files and GRO-Seq Analysis Workflow Source: https://github.com/nf-core/nascent/blob/main/docs/output.md HOMER (Hypergeometric Optimization of Motif EnRichment) is a comprehensive suite for Motif Discovery and next-gen sequencing analysis. The nf-core/nascent pipeline specifically supports the HOMER groseq workflow, generating various output files including bed, peaks, bedGraph, and tagdir for transcript identification. ```APIDOC transcript_identification/homer/: *.bed: HOMER Nascent RNA (GroSeq) transcripts after pos2bed *.peaks.txt: HOMER Nascent RNA (GroSeq) transcripts *.bedGraph.gz: UCSC bedGraph *_tagdir: homer tagdir ``` -------------------------------- ### Define Multipart MIME Email Structure Source: https://github.com/nf-core/nascent/blob/main/assets/sendmail_template.txt This snippet defines the standard email headers and the initial boundary for a multipart/related MIME email. It sets up the basic structure for embedding various content types like HTML and attachments, using placeholders for dynamic values such as recipient email and subject. ```MIME To: $email Subject: $subject Mime-Version: 1.0 Content-Type: multipart/related;boundary="nfcoremimeboundary" --nfcoremimeboundary Content-Type: text/html; charset=utf-8 $email_html ``` -------------------------------- ### RSeQC: RNA-seq Quality Control Modules Source: https://github.com/nf-core/nascent/blob/main/docs/output.md This section introduces RSeQC, a package of scripts designed to evaluate the quality of RNA-seq data. The pipeline runs several RSeQC scripts by default, which can be customized using the --rseqc_modules parameter. The majority of these scripts generate output files suitable for plotting and summarization in the MultiQC report. ```APIDOC Supported RSeQC modules (default via --rseqc_modules): bam_stat.py inner_distance.py infer_experiment.py junction_annotation.py junction_saturation.py read_distribution.py read_duplication.py Output: Majority of scripts generate files which can be plotted and summarised in the MultiQC report. ``` -------------------------------- ### UMI-tools dedup: Output Files and Process Source: https://github.com/nf-core/nascent/blob/main/docs/output.md This section describes the UMI-tools dedup command, which is used to deduplicate reads based on both mapping and UMI barcode information. It generates a filtered BAM file after the removal of PCR duplicates and various UMI-level statistics. This step follows UMI extraction. ```APIDOC Output files: / .umi_dedup.sorted.bam: If --save_umi_intermeds is specified, the UMI deduplicated, coordinate sorted BAM file containing read alignments. .umi_dedup.sorted.bam.bai: If --save_umi_intermeds is specified, the BAI index file for the UMI deduplicated, coordinate sorted BAM file. .umi_dedup.sorted.bam.csi: If --save_umi_intermeds --bam_csi_index is specified, the CSI index file for the UMI deduplicated, coordinate sorted BAM file. /umitools/ *_edit_distance.tsv: Reports the (binned) average edit distance between the UMIs at each position. *_per_umi.tsv: UMI-level summary statistics. *_per_umi_per_position.tsv: Tabulates the counts for unique combinations of UMI and position. ``` -------------------------------- ### Conditionally Embed Base64 Encoded MultiQC Report as Attachment Source: https://github.com/nf-core/nascent/blob/main/assets/sendmail_template.txt This Groovy template code checks for the existence and size of a MultiQC report file. If the file is present and within a specified maximum size, it reads the file, encodes its bytes into Base64, and includes it as an attachment within the multipart MIME email. The encoded data is formatted into 76-character lines for email compatibility. ```Groovy <%\nif (mqcFile){\ndef mqcFileObj = new File("$mqcFile")\nif (mqcFileObj.length() < mqcMaxSize){\nout << """\n--nfcoremimeboundary\nContent-Type: text/html; name=\"multiqc_report\"\nContent-Transfer-Encoding: base64\nContent-ID: \nContent-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"\n\n${mqcFileObj.\n bytes.\n encodeBase64().\n toString().\n tokenize( '\n' )*.\n toList()*.\n collate( 76 )*.\n collect { it.join() }.\n flatten().\n join( '\n' )}\n"""\n}}\n%> ``` -------------------------------- ### BEDTools Genomecov Output Files for Coverage Graphs Source: https://github.com/nf-core/nascent/blob/main/docs/output.md BEDTools Genomecov generates sample coverage files in bedGraph format, suitable for visualizing coverage graphs. It provides separate files for negative and positive strand coverage, as well as a dreg format prepared using the proseq2.0 pipeline. ```APIDOC coverage_graphs/: *.minus.bedGraph: Sample coverage file (negative strand only) in bedGraph format *.plus.bedGraph: Sample coverage file (positive strand only) in bedGraph format *.dreg.bedGraph: Sample coverage file (dreg) in bedGraph format prepared using proseq2.0 pipeline ``` -------------------------------- ### Configure HOMER GRO-seq Parameters in Nextflow Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This Nextflow configuration snippet demonstrates how to set specific parameters for the HOMER_FINDPEAKS process when the assay type is GRO-seq. It defines tssFold and bodyFold values, which are crucial for transcript identification. ```nextflow withName: HOMER_FINDPEAKS { ext.args = "-style groseq -tssFold 4 -bodyFold 3" } ``` -------------------------------- ### Limit Nextflow Java Memory Usage Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This snippet sets the NXF_OPTS environment variable to limit the Java Virtual Machine's initial and maximum memory allocation for Nextflow, preventing excessive memory consumption. It is recommended to add this to your shell's profile file (e.g., ~/.bashrc or ~/.bash_profile). ```bash NXF_OPTS='-Xms1g -Xmx4g' ``` -------------------------------- ### Picard MarkDuplicates: Duplicate Marking and Output Files Source: https://github.com/nf-core/nascent/blob/main/docs/output.md This section details the picard MarkDuplicates tool, which marks duplicate reads identified amongst alignments to gauge the overall level of duplication. For RNA-seq data, it is generally not recommended to physically remove duplicates unless UMIs are used, due to expected biological duplication. This step can be skipped using the --skip_markduplicates parameter. ```APIDOC Output files: / .markdup.sorted.bam: Coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM file and is saved by default. .markdup.sorted.bam.bai: BAI index file for coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM index file and is saved by default. .markdup.sorted.bam.csi: CSI index file for coordinate sorted BAM file after duplicate marking. Only generated if --bam_csi_index is specified. /samtools_stats/ SAMtools .markdup.sorted.bam.flagstat SAMtools .markdup.sorted.bam.idxstats SAMtools .markdup.sorted.bam.stats: Files generated from the duplicate marked alignment files. /picard_metrics/ .markdup.sorted.MarkDuplicates.metrics.txt: Metrics file from MarkDuplicates. ``` -------------------------------- ### Embed Base64 Encoded Image in Multipart Email Source: https://github.com/nf-core/nascent/blob/main/assets/sendmail_template.txt This Groovy template code reads a local image file, encodes its bytes into Base64, and formats the output to be included as an inline attachment within a multipart MIME email. It ensures the image data is properly chunked into 76-character lines for email compatibility, referencing the project directory for the image path. ```Groovy <% out << new File("$projectDir/assets/nf-core-nascent_logo_light.png"). bytes. encodeBase64(). toString(). tokenize( '\n' )*. toList()*. collate( 76 )*. collect { it.join() }. flatten(). join( '\n' ) %> ``` -------------------------------- ### Update Cached nf-core/nascent Pipeline Version Source: https://github.com/nf-core/nascent/blob/main/docs/usage.md This command ensures that the local cached version of the nf-core/nascent pipeline is updated to the latest available version from GitHub. It is crucial for accessing new features, bug fixes, and improvements. ```bash nextflow pull nf-core/nascent ``` -------------------------------- ### Nextflow Pipeline Execution Status Reporting Logic Source: https://github.com/nf-core/nascent/blob/main/assets/email_template.html This snippet shows the Groovy/Nextflow templating logic used to generate the success or failure message in the pipeline report. It checks the 'success' variable and displays detailed error information, including exit status and error report, if the workflow failed. ```Nextflow <% if (!success){ out << """ #### nf-core/nascent execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: `$exitStatus`. The full error message was: ${errorReport} """ } else { out << """ nf-core/nascent execution completed successfully! """ } %> ``` -------------------------------- ### Filter Distal TREs using BEDTools intersect Source: https://github.com/nf-core/nascent/blob/main/docs/output.md This command uses BEDTools intersect to identify distal transcriptional regulatory elements (TREs) by excluding regions that overlap with known promoter regions. The `-v` option reports entries in file A that do not overlap with any entry in file B, effectively isolating distal elements. ```Shell bedtools intersect -a SampleA_1_bidirectional_peaks.bed -b promoters.bed -v > SampleA_1_bidirectional_peaks.distalTREs.bed ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.