nf-core/cageseq

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Custom MultiQC yaml file containing HTML including a methods description.

Run the whole pipeline

Run only the mapping part until bigiwgs or bams

Run only the CAGEr processing part from bigiwgs or bams

Genome annotation fiel in GTF format

Path to the input file. Mutually exclusive with infolder

Path to the folder with fastq files. Mutually exclusive with input

Whether to save merged fasta files

Number of underscore separated fields denoting sample name when infolder is used

Name of the reference genome. It is used as meta information

FASTA file containing a reference genome.

Specifies a directory with a genome index

Sequencing platform used. Required for mapping with STAR

Name of the sequencing center. Required for mapping with STAR

Whether only uniquely mapped reads should be considered for downstream analysis.

Whether to keep only those reads that start with G base

Additional parameters that can be passed to TrimGalore!

Makes the pipeline skip the G-trimming step in preprocessing

Switches the aligner from STAR to bowtie2

Switches on PCR duplicate removal

Sets an optical duplicate distance, used together with dedup

The input CSV samplesheet including the name of the samples, their pairedness status, and the location of bigwig or bam files. Required when cageronly is true.

Format of the mapping data file passed to the TSS analysis part when STAR is used (either ‘bam’ or ‘bigwig’).

Seed file for BSgenome forging

Directory containing either a set of FASTA files, one per reference chromosome, or a 2bit file for the whole reference genome. Used for BSgenome forging

BSgenome R package to use (if not forged)

Threshold above which raw and normalized CTSS are considered for the correlation plot

Defines the lower thresold for fitting the power-law distribution

Defines the upper thresold for fitting the power-law distribution

Method used for normalizing the samples: powerLaw, simpleTpm, and none are supported

User specified alpha, the -1 * fitted slope in the log-log representation of the power-law distribution. If none, the average across samples is calculated and used.

Total number of CAGE tags in the reference power-law distribution

Parameters for filtering low expressed CTSS before clustering. ctss_thr specifies the lower threshold above which CTSS are considered, and sample_num_thr specifies the number of samples where this threshold should be passed.

Parameters for filtering low expressed CTSS before clustering. ctss_thr specifies the lower threshold above which CTSS are considered, and sample_num_thr specifies the number of samples where this threshold should be passed.

Maximum distance for distance-based clustering (distclu)

The tpm threshold above which even a single CTSS is kept during clustering

Define the lower quantile boundaries of the interquartile range

Define the upper quantile boundaries of the interquartile range

Threshold above which tag clusters are considered for the interquartile width distribution plot

Upstream distance to consider into TSS region for ChIPseeker annotation

Downstream distance to consider into TSS region for ChIPseeker annotation

The number of bases to inlcude upstream of the TSS for TSS logos

Used for defining the consensus clusters. consensus_thr specifies the TPM threshold above which tag clusters are considered for consensus clusters, and consensus_dist define the maximum distance between the interquartile ranges of tag clusters to be joined together into consensus clusters.

Used for defining the consensus clusters. consensus_thr specifies the TPM threshold above which tag clusters are considered for consensus clusters, and consensus_dist define the maximum distance between the interquartile ranges of tag clusters to be joined together into consensus clusters.

Defines the balance threshold above which bidirectionality is considered balanced and enhancers are called

Used for selecting only supported enhancers. unexpressed is a non inclusive lower TPM boundary for expression when calculating support of enhancers. minSamples is a non-inclusive lower boundary for the number of samples where the clusters should show bidirectionality.

Used for selecting only supported enhancers. unexpressed is a non inclusive lower TPM boundary for expression when calculating support of enhancers. minSamples is a non-inclusive lower boundary for the number of samples where the clusters should show bidirectionality.