nf-core/atacseq

Path to comma-separated file containing information about the samples in the experiment.

Specifies that the input is single-end reads.

Estimated fragment size used to extend single-end reads.

Sequencing center information to be added to read group of BAM files.

Path to the output directory where the results will be saved.

Email address for completion summary.

Name of iGenomes reference.

Path to Fasta reference file.

Path to GTF annotation file.

Full path to directory containing BWA index including base name. i.e. /path/to/index/genome.fa.

Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

Path to BED file containing transcription start sites. This will be created from the gene BED file if not specified.

Effective genome size parameter required by MACS2.

Path to blacklist regions in BED format, used for filtering alignments.

Name of Mitochondrial chomosome in reference assembly e.g. chrM.

If generated by the pipeline save the BWA index in the results directory.

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

Skip the adapter trimming step.

Save the trimmed FastQ files in the results directory.

Reads mapping to mitochondrial contig are not filtered from alignments.

Duplicate reads are not filtered from alignments.

Reads mapping to multiple locations are not filtered from alignments.

Don’t output BWA MEM alignments with score lower than this parameter.

Do not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.

Save the intermediate BAM files from the alignment step.

Run MACS2 in narrowPeak mode.

Specifies broad cutoff value for MACS2. Only used when —narrow_peak isnt specified.

Minimum FDR (q-value) cutoff for peak detection, —macs_fdr and —macs_pvalue are mutually exclusive.

p-value cutoff for peak detection, —macs_fdr and —macs_pvalue are mutually exclusive. If —macs_pvalue cutoff is set, q-value will not be calculated and reported as -1 in the final .xls file.

Number of biological replicates required from a given condition for a peak to contribute to a consensus peak.

Instruct MACS2 to create bedGraph files normalised to signal per million reads.

Skip MACS2 peak QC plot generation.

Skip annotation of MACS2 and consensus peaks with HOMER.

Skip consensus peak generation, annotation and counting.

Use vst transformation instead of rlog with DESeq2.

Skip differential accessibility analysis.

Skip FastQC.

Skip Picard CollectMultipleMetrics.

Skip Preseq.

Skip deepTools plotProfile.

Skip deepTools plotFingerprint.

Skip Ataqv.

Skip IGV.

Skip MultiQC.