ramdaq: Usage: Using test data

Below commands automatically download annotation data and test FASTQ data and run the pipeline.

Currently, 8 combinations of annotations/data types are availabe:

• Species: mouse and human
• Sequencing: single-end and paired-end
• Strandness: unstranded and stranded (fr-firststrand)

mouse, single-end

mouse, single-end, unstranded

nextflow run rikenbit/ramdaq -profile test_SE_UST_M,docker --outdir results_DLtest_SE_UST_M

mouse, single-end, stranded

nextflow run rikenbit/ramdaq -profile test_SE_ST_M,docker --outdir results_DLtest_SE_ST_M

mouse, paired-end

mouse, paired-end, unstranded

nextflow run rikenbit/ramdaq -profile test_PE_UST_M,docker --outdir results_DLtest_PE_UST_M

mouse, paired-end, stranded

nextflow run rikenbit/ramdaq -profile test_PE_ST_M,docker --outdir results_DLtest_PE_ST_M

human, single-end

human, single-end, unstranded

nextflow run rikenbit/ramdaq -profile test_SE_UST_H,docker --outdir results_DLtest_SE_UST_H

human, single-end, stranded

nextflow run rikenbit/ramdaq -profile test_SE_ST_H,docker --outdir results_DLtest_SE_ST_H

human, paired-end

human, paired-end, unstranded

nextflow run rikenbit/ramdaq -profile test_PE_UST_H,docker --outdir results_DLtest_PE_UST_H

human, paired-end, stranded

nextflow run rikenbit/ramdaq -profile test_PE_ST_H,docker --outdir results_DLtest_PE_ST_H