run-dedup-demultiplex-examples.md

Run UMI extraction, deduplication and demultiplexing examples

Examples of configurations that request that the riboviz workflow do UMI extraction and deduplication and also demultiplexing of multiplexed data are provided. These use Simulated FASTQ test files located within data/simdata/.

Note: These currently do not output normalized_density_APEsites_per_codon.pdf|tsv during the invocation of generate_stats_figs.R. This is a tiny mock data with very few reads and failures arise if these files are requested.

UMI extraction and deduplication

vignette/simdata_umi_config.yaml has a sample configuration file which runs an analysis of data/simdata/umi5_umi3_umi_adaptor.fastq with UMI extraction and deduplication enabled.

To run this example using the Nextflow workflow:

$ nextflow run prep_riboviz.nf -params-file vignette/simdata_umi_config.yaml -ansi-log false

Barcode and UMI extraction, demultiplexing and deduplication

vignette/simdata_multiplex_config.yaml has a sample configuration file which runs an analysis of data/simdata/multiplex.fastq with barcode and UMI extraction, demultiplexing and deduplication enabled.

To run this example using the Nextflow workflow:

$ nextflow run prep_riboviz.nf -params-file vignette/simdata_multiplex_config.yaml -ansi-log false