PAREsnip2 Data Input

To perform an analysis using PAREsnip2 for a specific organism, the user must input the following data:

• a reference file (transcriptome) in either FASTA format or Generic Feature Format version 3 (GFF3) with corresponding genome;
• a genome file (optional unless using GFF3 as reference);
• one or more sRNA library replicates;
• one or more degradome library replicates

A reference file and at least one sRNA and degradome library are required to perform an analysis. If the user chooses to use a GFF3 file as a reference then a corresponding genome must also be provided.  When extracting the gene sequences from the genome using a GFF3, the user has the option to include or exclude untranslated regions (UTRs).

The sRNA and degradome libraries must be in redundant FASTA format with the adapters trimmed.

Analysis Configuration

A description of the analysis configuration parameters and their meaning can be found in the user manual.