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Merge branch 'main' of github.com:bcgsc/rAMPage into main
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@dy-lin
dy-lin committed Jan 19, 2022
2 parents 5534618 + a637384 commit d536148
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38 changes: 19 additions & 19 deletions README.md
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Expand Up @@ -324,25 +324,25 @@ USAGE(S):
rAMPage.sh [-a <address>] [-b] [-c <taxonomic class>] [-d] [-f] [-h] [-m] [-n <species name>] [-o <output directory>] [-p] [-r <FASTA.gz>] [-s] [-t <int>] [-v] <input reads TXT file>
OPTIONS:
-a <address> email address for alerts
-b benchmark (uses /usr/bin/time -pv)
-c <class> taxonomic class of the dataset (default = top-level directory in $outdir)
-d debug mode of Makefile
-f force characterization even if no AMPs found
-h show help menu
-m <target> Makefile target (default = exonerate)
-n <species> taxonomic species or name of the dataset (default = second-level directory in $outdir)
-o <directory> output directory (default = directory of input reads TXT file)
-p run processes in parallel
-r <FASTA.gz> reference transcriptome (accepted multiple times, *.fna.gz *.fsa_nt.gz)
-s strand-specific library construction (default = false)
-t <int> number of threads (default = 48)
-v print version number
-E <e-value> E-value threshold for homology search (default = 1e-5)
-S <0 to 1> AMPlify score threshold for amphibian AMPs (default = 0.90)
-L <int> Length threshold for AMPs (default = 30)
-C <int> Charge threshold for AMPs (default = 2)
-a <address> email address for alerts
-c <class> taxonomic class of the dataset (default = top-level directory in $outdir)
-d debug mode of Makefile
-f force characterization even if no AMPs found
-h show help menu
-m <target> Makefile target (default = exonerate)
-n <species> taxonomic species or name of the dataset (default = second-level directory in $outdir)
-o <directory> output directory (default = directory of input reads TXT file)
-p run processes in parallel
-r <FASTA.gz> reference transcriptome (accepted multiple times, *.fna.gz *.fsa_nt.gz)
-s strand-specific library construction (default = false)
-t <int> number of threads (default = 48)
-v print version number
-E <e-value> E-value threshold for homology search (default = 1e-5)
-S <0 to 1> AMPlify score threshold for amphibian AMPs (default = 0.90)
-L <int> Length threshold for AMPs (default = 30)
-C <int> Charge threshold for AMPs (default = 2)
-R Disable redundancy removal during transcript assembly
EXAMPLE(S):
rAMPage.sh -a [email protected] -c class -n species -p -s -t 8 -o /path/to/output/directory -r /path/to/reference.fna.gz -r /path/to/reference.fsa_nt.gz /path/to/input.txt
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6 changes: 3 additions & 3 deletions scripts/README.md
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Expand Up @@ -139,14 +139,14 @@ DESCRIPTION:
For more information: https://github.com/bcgsc/RNA-Bloom
USAGE(S):
run-rnabloom.sh [-a <address>] [-m <int K/M/G>] [-s] [-t <int>] -o <output directory> <reads list TXT file>
run-rnabloom.sh [-a <address>] [-d] [-h] [-m <int K/M/G>] [-s] [-t <int>] -o <output directory> <reads list TXT file>
OPTION(S):
-a <address> email address for alerts
-d debug mode
(skips RNA-Bloom)
-d debug mode (skips RNA-Bloom)
-h show help menu
-m <int K/M/G> allotted memory for Java (e.g. 500G)
-n no redundancy removal
-o <directory> output directory (required)
-s strand-specific library construction (default = false)
-t <int> number of threads (default = 8)
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