transigner

Quantify RNA in long-read FASTQ files using TranSigner

usage

nexus run --nf-workflow quantification_transigner.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_transcripts_fasta_file /path/to/file.fasta \
    --params_transigner_align "" \
    --params_transigner_prefilter "--filter -tp -500 -fp -600" \
    --params_transigner_em "--drop --use-score"

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’.
--output_dir	Directory to which output files will be copied.
--reference_transcripts_fasta_file	Reference transcripts FASTA file.
--params_transigner_align	TranSigner align parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--params_transigner_prefilter	TranSigner prefilter parameters (default: ‘“–filter -tp -500 -fp -600”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--params_transigner_em	TranSigner em parameters (default: ‘“–drop –use-score”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.