kallisto-pe

Quantify RNA in pairend-end read FASTQ files using Kallisto

usage

nexus run --nf-workflow quantification_kallisto-pe.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_transcripts_fasta_file /path/to/file.fasta \
    --params_kallisto_index "-k 31" \
    --params_kallisto_quant ""

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fastq_file_1’, ‘fastq_file_2’.
--reference_transcripts_fasta_file	Reference transcripts FASTA file.
--output_dir	Directory to which output files will be copied.
--params_kallisto_quant	Kallisto quant parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.