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The FASTX Toolkit provides a set of command line tools for manipulating both FASTA and FASTQ files. The available modules are described on their website. They include a fast fastx_trimmer utility for trimming FASTQ sequences (and quality score strings) before alignment.

Data staging

Set up to process the yeast data if you haven't already.

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Info

You must tell any adapter trimming program what your R1 and R2 adapters look like.

The GSAF website describes the flavors of Illumina adapter and barcode sequences in more detail:  Illumina - all flavors (USE with Caution, this is outdated but can be useful for a basic understanding of the adapters, the GSAF primarily only uses UDI's for all projects).

The cutadapt program is an excellent tool for removing adapter contamination. It is available as a BioContainers module.

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Figuring out which adapter sequence to use when can be tricky. Your sequencing provider can tell you what adapters they used to prep your libraries. For GSAF's adapter layout, please refer to Illumina - all flavors (USE with Caution, this is outdated but can be useful for a basic understanding of the adapters, the GSAF primarily only uses UDI's for all projects) (you may want to read all the "gory details" below later).

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