nf-core/atacseq

You will need to create a samplesheet with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. See usage docs.

Read length together with the genome fasta are used to calculate MACS3 genome size using the khmer program as explained here. For all the genomes present in the igenomes.config the genome size has been already precomputed and the read length is then used to retrieve the corresponding value

Use this to indicate that your samplesheet lists controls.

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

This parameter is mandatory if --genome is not specified. If you don't have the appropriate alignment index available this will be generated for you automatically. Combine with --save_reference to save alignment index for future runs.

This parameter is mandatory if --genome is not specified.

This parameter must be specified if --genome or --gtf are not specified.

Effective genome size parameter required by MACS3. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. For other genomes, if this parameter is not specified then the MACS3 peak-calling and differential analysis will be skipped.

If provided, alignments that overlap with the regions in this file will be filtered out (see ENCODE blacklists). The file should be in BED format. Blacklisted regions for GRCh37, GRCh38, GRCm38, hg19, hg38, mm10 are bundled with the pipeline in the blacklists directory, and as such will be automatically used if any of those genomes are specified with the --genome parameter.

Reads aligning to this contig are filtered out if a valid identifier is provided otherwise this step is skipped. Where possible these have been provided in the igenomes.config.

If the index generated by the aligner is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.

By default takes the value of the mito_name parameter, if set. However, some plants and algae have chloroplast genomes in addition to a mitochondrial genome and thus mito_name can have values as multiple names that are separated by a | symbol that will break ataqv, in these cases this parameter can be used to overwrite these values.

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.

By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.

An additional series of steps are performed by the pipeline for merging the replicates from the same experimental group. This is primarily to increase the sequencing depth in order to perform downstream analyses such as footprinting. Specifying this parameter means that these steps will not be performed.

By default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set this parameter to also save other intermediate BAM files.

This may either be in the form of FastQ or BAM files depending on the options available for that particular tool.

Shift aligned reads as commonly done for ATACseq footprinting analysis, +4 bp for reads on the + strand, -5 bp for reads on the - strand. This can only be applied if all samples are paired-end.

MACS3 is run by default with the --broad flag. Specify this flag to call peaks in narrowPeak mode.

If you are confident you have good reproducibility amongst your replicates then you can increase the value of this parameter to create a 'reproducible' set of consensus peaks. For example, a value of 2 will mean peaks that have been called in at least 2 replicates will contribute to the consensus set of peaks, and as such peaks that are unique to a given replicate will be discarded.

See DESeq2 docs.