| | Input FASTQ files for the forward reads. All FASTQ file names must start with the prefix '{well_id}_R1', where
'well_id' can be found as the sequence identifier in the barcodes FASTA file (see 'barcodesFasta' argument).
For each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the 'input_r2' argument,
meaning that their 'well_id' prefix must match. The number of items provided for 'input_r1' must be equal
to the number of items for 'input_r2'.
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| | Input FASTQ files for the reverse reads. All FASTQ file names must start with the prefix '{well_id}_R2', where
'well_id' can be found as the sequence identifier in the barcodes FASTA file (see 'barcodesFasta' argument).
For each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the 'input_r1' argument,
meaning that their 'well_id' prefix must match. The number of items provided for 'input_r1' must be equal
to the number of items for 'input_r2'.
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| | Reference genome to match to. Can be generated from genomic FASTA sequences and a genome annotation
by using STAR with '--runMode genomeGenerate'.
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| | FASTA file where each entry specifies a unique barcode sequence present at the start of the forward input reads
(input_r1). The IDs of each barcode (the start of the FASTA headers up until the first whitespace character) must
match with the start of one input FASTQ pair.
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