salmon-fastq

Quantify RNA in paired-end FASTQ files using Salmon

usage

nexus run --nf-workflow quantification_salmon-fastq.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_transcripts_fasta_file /path/to/file.fasta \
    --params_salmon_index "--gencode" \
    --params_salmon_quant "--libType IU --seqBias --gcBias --posBias"

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’.
--output_dir	Directory to which output files will be copied.
--reference_transcripts_fasta_file	Reference transcripts FASTA file.
--params_salmon_index	Salmon index parameters (default: ‘“–gencode”’). Note that the parameters need to be wrapped in quotes.
--params_salmon_quant	Salmon parameters (default: ‘“–libType IU –seqBias –gcBias –posBias”’). Note that the parameters need to be wrapped in quotes.