https://bioinformaticsonline.com/snippets/view/37293/running-transrate? https://bioinformaticsonline.com/snippets/view/37293/running-transrate Fri, 13 Jul 2018 07:55:46 -0500 https://bioinformaticsonline.com/snippets/view/37293/running-transrate ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate _ _ | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___ ░▓▓▓^▓▓▓░ | __|| '__|/ _` || '_ \ / __|| '__|/ _` || __|/ _ \ ░▓▓▓^▓▓▓░ ░▓▓▓^▓▓▓░ | |_ | | | (_| || | | |\__ \| | | (_| || |_| __/ ░▓▓▓^▓▓▓░ ░▓▓▓^▓▓▓░ \__||_| \__,_||_| |_||___/|_| \__,_| \__|\___| ░▓▓▓^▓▓▓░ Transrate v1.0.3 by Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian Hibberd, and Steve Kelly DESCRIPTION: Analyse a de-novo transcriptome assembly using three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping based (if --left and --right are given) 3. reference based (if --reference is given) Documentation at http://hibberdlab.com/transrate USAGE: transrate <options> OPTIONS: --assembly=<s> Assembly file(s) in FASTA format, comma-separated --left=<s> Left reads file(s) in FASTQ format, comma-separated --right=<s> Right reads file(s) in FASTQ format, comma-separated --reference=<s> Reference proteome or transcriptome file in FASTA format --threads=<i> Number of threads to use (default: 8) --merge-assemblies=<s> Merge best contigs from multiple assemblies into file --output=<s> Directory where results are output (will be created) (default: transrate_results) --loglevel=<s> Log level. One of [error, info, warn, debug] (default: info) --install-deps=<s> Install any missing dependencies. One of [ref] --examples Show some example commands with explanations ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate --assembly=Trinity.fasta --output=transrateSTAT [ INFO] 2018-07-13 14:54:03 : Loading assembly: /media/urbe/MyPassport/BorisTrinityAssembly/Trinity.fasta [ INFO] 2018-07-13 14:54:21 : Analysing assembly: /media/urbe/MyPassport/BorisTrinityAssembly/Trinity.fasta [ INFO] 2018-07-13 14:54:21 : Results will be saved in /media/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trinity [ INFO] 2018-07-13 14:54:21 : Calculating contig metrics... [ INFO] 2018-07-13 14:54:34 : Contig metrics: [ INFO] 2018-07-13 14:54:34 : ----------------------------------- [ INFO] 2018-07-13 14:54:34 : n seqs 98389 [ INFO] 2018-07-13 14:54:34 : smallest 201 [ INFO] 2018-07-13 14:54:34 : largest 22136 [ INFO] 2018-07-13 14:54:34 : n bases 147938374 [ INFO] 2018-07-13 14:54:34 : mean len 1503.61 [ INFO] 2018-07-13 14:54:34 : n under 200 0 [ INFO] 2018-07-13 14:54:34 : n over 1k 53685 [ INFO] 2018-07-13 14:54:34 : n over 10k 88 [ INFO] 2018-07-13 14:54:34 : n with orf 61028 [ INFO] 2018-07-13 14:54:34 : mean orf percent 61.07 [ INFO] 2018-07-13 14:54:34 : n90 748 [ INFO] 2018-07-13 14:54:34 : n70 1578 [ INFO] 2018-07-13 14:54:34 : n50 2286 [ INFO] 2018-07-13 14:54:34 : n30 3182 [ INFO] 2018-07-13 14:54:34 : n10 4912 [ INFO] 2018-07-13 14:54:34 : gc 0.33 [ INFO] 2018-07-13 14:54:34 : bases n 0 [ INFO] 2018-07-13 14:54:34 : proportion n 0.0 [ INFO] 2018-07-13 14:54:34 : Contig metrics done in 13 seconds [ INFO] 2018-07-13 14:54:34 : No reads provided, skipping read diagnostics [ INFO] 2018-07-13 14:54:34 : No reference provided, skipping comparative diagnostics [ INFO] 2018-07-13 14:54:34 : Writing contig metrics for each contig to /media/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trinity/contigs.csv [ INFO] 2018-07-13 14:54:40 : Writing analysis results to assemblies.csv]]> Jit