Setting Mandatory parameters using Shiny

Using the Rshiny application to configure zUMIs YAML files makes it really easy to set up your zUMIs runs.

Here, we will walk through the mandatory parameters for each run.

• Name of the run/project: This name will be used to label output files produced by zUMIs.
• Path to the output directory: All output files will be stored in this directory. Please remember to give the full path, as relative paths may not work.
• Number of input fastq files: Drag the slider to set how many fastq files (Read and Index) are generating during sequencing. You will see that for each fastq file, fields for the path and for the base definition will appear.
• Path to fastq files: Please remember to give full paths, as relative paths may not work.
• BC (Barcode definition): List any barcode (BC) ranges to be extracted from the reads in the box corresponding to the correct fastq file. You can also extract several barcode ranges from the same read using comma-separation: 1-6,11-16
• UMI (UMI definition): List any unique molecular identifier (UMI) ranges to be extracted from the reads.
• cDNA (cDNA sequence): List the cDNA range(s) in the reads to be mapped to the genome. May be one range (single-end) or two ranges (paired-end).

• Full path to the STAR index directory: The STAR index should be generated without splice junction database. Please remember to give the full path, as relative paths may not work.
• Full path to the annotation GTF file: Make sure the gene annotation matches the genome. Please remember to give the full path, as relative paths may not work.
• OPTIONAL: Additional mapping parameters for STAR: Here you can add custom mapping parameters, as mentioned elsewhere. For instance, try trimming adapter sequenes using --clip3pAdapterSeq
• OPTIONAL: Number of additional reference sequences: Here you can give additional reference sequences zUMIs should map to but are not integrated in the STAR index. For instance, you could add the ERCC spike-in reference on the fly (eg. ERCC.fa). For the number of additional sequences specified, a field for the path will appear.