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Running Transrate !
By Jit 2115 days ago
➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate
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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
