kallisto-lr

Quantify RNA in long-read FASTQ files using Kallisto

usage

nexus run --nf-workflow quantification_kallisto-lr.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_transcripts_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --params_kallisto_index "-k 63" \
    --params_kallisto_bus "-x bulk --threshold 0.8" \
    --params_bustools_sort "" \
    --params_bustools_count "--cm -m" \
    --params_kallisto_quanttcc "-P PacBio --matrix-to-files"

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’.
--reference_transcripts_fasta_file	Reference transcripts FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--output_dir	Directory to which output files will be copied.
--params_kallisto_index	Kallisto index parameters (default: ‘“-k 63”’).
--params_kallisto_bus	Kallisto bus parameters (default: ‘“-x bulk –threshold 0.8”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--params_bustools_sort	Bustools sort parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--params_bustools_count	Bustools count parameters (default: ‘“–cm -m”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--params_kallisto_quanttcc	Kallisto quant-tcc parameters (default: ‘“-P PacBio –matrix-to-files”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.