RMAP
How to download the tool or source code including installation and usage instructions as well as any source code that might be associated with the executable. This should also include a listing of any dependencies for this tool or script.
- Download the RMAP package from http://smithlab.cmb.usc.edu/smithlab/index.php/software/rmap to a directory.
- tar -jxvf filename
- RMAP requires 64-bit machine and GCC version ? 4.1 (to support TR1).
Required version of the program necessary to perform the desired task
- RMAP v2.05
Sample dataset and expected results to be output
- Excerpt from sample input files, chr8.fa (fasta file, reference sequence), and test_reads_bs.fq (fastq file, short reads)
chr8.fa: >chr8 GCAATTATGACACAAAAAATTAAACAGTGCAGACTGATATATAAATCAAA ACAAATGTCCTTTACATGTTTTCTGTTACAGTAGTAACAATATGTGTAAA CTTAATTATCATATTTTTTTCTTGTGCTGTGGTTGTGTCCTGGGTTCATT CTCTAAAATGCTGTTCACCTTAGACCAGGAGAAATATTAACCATACAGAC TCTGTTTCAAGTCATAGCTGAATATTTTCAAAAGAGTGACTTTGTAAAAA CATGTTCCAATGGCAAATTGATTCATTGTGATGGGATCAATTATTCCAAA GACTTCTTGTCTTTATTTTGTTCCCATGCCTACCTTTTAGCCATAATACA
test_reads_bs.fq: @chr8:144-169_1_0000000000000000000000000_0 TTTATTTTTTAAAATGTTGTTTATT \+chr8:144-169_1_0000000000000000000000000_0 OhhhKhhhhLhhhhhhhhhhRhhhh @chr8:440-465_1_0000000000000000000000000_0 TATAATGTTTTTTAAAATAAAAGAG \+chr8:440-465_1_0000000000000000000000000_0 QhhhhhhhhhhhhOhHhhhhhhhhh @chr8:1759-1784_0_0000000000000000000000000_0 TTGTAGGTTATTGAGGAAGGTGAGG \+chr8:1759-1784_0_0000000000000000000000000_0 XhNh\[ZhhhhhhQThhKRhhhhhhh
- Excerpt from sample output files, test_reads_bs.bed
test_reads_bs.bed: chr8 2433 2458 chr8:2433-2458_0_0000000000000000000000000_0 0.2 - chr8 4690 4715 chr8:4690-4715_0_0000000000000000000000000_0 0.2 - chr8 293 318 chr8:293-318_0_0000000000000000000000000_0 0.133333 - chr8 466 491 chr8:466-491_0_0000000000000000000000000_0 0.133333 -
- Excerpt from sample input files, chr8.fa (fasta file, reference sequence), and test_reads_bs.fq (fastq file, short reads)
Set of parameters and command line switches that match the expected execution of the tool including the possible command line definitions according to the occurrence of optional parameters. Also, validation instructions for parameters are requested.
- Running the rmapbs
- USAGE:
rmapbs [OPTIONS] <fast[a/q]-reads-file>
- OPTIONS:
parameter
brief description of the parameter
required
default value
text, number, or file/path
description of validation rules
-o, -output
Name of output file
N
stdout
file
-c, -chrom
FASTA file or dir containing chromosome(s)
Y
none
file/path
-s, -suffix
suffix of FASTA files (assumes -c indicates dir)
N
none
-F, -filenames
file listing names of chromosome files
N
none
file
-p, -prb
file with quality scores (prb format)
N
none
file
-S, -seeds
number of seeds
N
3
integer
>= 1
-h, -hit
weight of hit
N
11
integer
>=1
-w, -width
width of reads
N
none
integer
>=1
-m, -mismatch
maximum allowed mismatches
N
10
integer
>=0
-a, -ambiguous
file to write names of ambiguously mapped reads
N
none
file
-M, -max-map
maximum allowed mappings for a read
N
1
integer
>=1
-W, -wc
run in wildcard matching mode
N
none
-P, -prob
wildcard cutoff probability
N
0.75
real
(0,1)
-Q, -qual
use quality scores (input must be FASTQ)
N
none
-A, -ag-wild
map using A/G bisulfite wildcards
N
none
-B, -bias
allow CpG non-conversion to assist
N
none
-f, -faster
faster seeds (sensitive to 2 mismatches)
N
none
-v, -verbose
print more run info
N
none
-?, -help
print this help message
N
none
- USAGE:
- Running the rmapbs
Example invocation of the command line application and its associated parameters such that it can perform an analysis
- Running the rmapbs
~/bin/rmap_v2.05/rmapbs -c chr8.fa -o test_reads_bs.bed test_reads_bs.fq
- Running rmapbs with prb data
~/bin/rmap_v2.05/rmapbs -Q -p test_reads_bs.prb -c chr8.fa -o test_reads_bs.bed test_reads_bs.fq
- Running rmapbs on reverse complement strand
~/bin/rmap_v2.05/rmapbs -A -Q -p test_reads_bs.prb -c chr8.fa -o test_reads_bs.bed test_reads_bs.fq
- Running the rmapbs