List of fastq files containing the first mate of raw reads. Muliple files are provided if multiplexing of the same library has been done on multiple lanes. The reads comming from different fastq files are pooled after alignment. Also see parameter \"fastq2\".

List of fastq files containing the second mate of raw reads. Important: this list has to be of same length as parameter \"fastq1\".

Path to reference genome in fasta format. Bowtie2 index files (\".1.bt2\", \".2.bt2\", ...) as well as a samtools index (\".fai\") has to be located in the same directory.\n All of these files can be downloaded for the most common genome builds at https://support.illumina.com/sequencing/sequencing_software/igenome.html. Alternatively, you can use \"bowtie2-build\" or \"samtools index\" to create them yourself.

Adapter sequence for first reads. If not specified (set to \"null\"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to \"illumina\", \"nextera\", or \"small_rna\". Or you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").

Adapter sequence for second reads. If not specified (set to \"null\"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to \"illumina\", \"nextera\", or \"small_rna\". Or you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").

Bin size used for generation of coverage tracks. The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1.

Sample ID used for naming the output files.

Path to a tab-delimited file listing chromosome sizes in following fashion:\n \"chromosome_name<tab>total_number_of_bp\".\n For the most common UCSC genome build, you can find corresponding files at: https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. Or you can generate them yourself using UCSC script fetchChromSizes (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion:\n \"fetchChromSizes hg38 > hg38.chrom.sizes\".\n If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using:\n \"awk -v OFS='\t' {'print $1,$2'} hg38.fa.fai > hg38.chrom.sizes\".

Q-value cutoff used for peak calling by MACS2. The default is 0.05.

The effectively mappable genome size, please see: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html

List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. Specify as space-delimited string. Default: \"chrX chrY chrM\"

Maximum insert length between two reads of a pair. In case of ATACseq, very long insert sizes are possible. So it is recommended to use at least a value of 1500. However, please note that alignment will take significantly longer for higher insert sizes. The default is 2500.