Documentation options are not the same as the current version (1.1.2) and are not recognised

[ulyssebaruchel]

Hi, when I try to use the software installed through bioconda (build h43eeafb_1), I get this text:

Required: -f STRING: fasta file containing the receptor genome sequence [Read file] -u STRING: path to single-end read file or -1 STRING -2 STRING: path to paried-end read files or -b STRING: path to BAM alignment file Optional: -o STRING: prefix of the output file (default: trust) -t INT: number of threads (default: 1) -c STRING: the path to the kmer count file -k INT: the starting k-mer size for indexing contigs (default: 9) --minHitLen INT: the minimal hit length for a valid overlap (default: auto) --skipMateExtension: skip the step of extension assemblies with mate-pair information --trimLevel INT: 0: no trim; 1: trim low quality; 2: trim unmatched (default: 1) --barcode STRING: the path to the barcode file (default: not used) --UMI STRING: the path to the UMI file (default: not used) --keepNoBarcode: assemble the reads with missing barcodes. (default: ignore the reads)

Many of the options described in the documentation and in some past issues are not recognised when I try to use them:

• '--read-format'
• '--ref'
• '--barcodeRange'
• '--umiRange'

I do not know how I can specify my UMI and cell barcode positions on one of my two reads (the other read containing the gene insert) from input FASTQ files. Can you tell me what options I should use, please? Thank you

[mourisl]

This is the "trust4" main executable for the assembly stage. You shall run trust4 through the wrapper "run-trust4". You can use the "--readFormat" option following the readme at: https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data . I

[ulyssebaruchel]

Great, thank you!