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splice_detection_man
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splice_detection_man
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.\" Manpage for splice_detection.
.TH man 1 "21 August 2014" "0.1" "splice_detection man page"
.SH NAME
splice_detection \- detect splicing in RNA sequencing data
.SH SYNOPSIS
splice_detection \-i inputfile \-g genome [options]
.SH DESCRIPTION
splice_detection is a program which detects splicing in RNA sequencing data. It looks for reads which do not match the genome continously by trying to find two distinct parts in any given read(part A and part B). In part A, it accepts relatively low mismatch rates without many mismatches in a row, while in part B it accepts high mismatch rates. If part B matches the genome closely at another location, this is accepted as a possible splice. If these conditions are not met the read is rejected as a possible splice.
.SH OPTIONS
.TP
.BI \-i,\-\-input " file_name"
input file containing reads from sequencing. This file should contain each read on a single line.
.TP
.BI \-g,\-\-genome " file_name"
input file containing the genome or gene of interest. The runtime of splice_detection will be greatly increased as this file becomes larger.
.TP
.BI \-l,\-\-status_log " file_name"
create current status log file. The number of currently processed reads will be written to file specified in increments of 10,000 reads.
.TP
.BI \-t,\-\-threads " integer"
specify number of processes (threads) to use for execution.
.TP
.BI \-s,\-\-seed_len " integer"
set initial seed length which must match the genome exactly for any given location.
.TP
.BI \-\-partA_min_len " integer"
minimum length for part A of reads.
.TP
.BI \-\-partB_min_len " integer"
minimum length for part B of reads.
.TP
.BI \-\-mM1_roof " float"
highest mismatch rate for part A which will not result in rejection. This value must be between zero and one.
.TP
.BI \-\-mM2_floor " float"
lowest mismatch rate for part B which will not result in rejection. This value must be between zero and one.
.TP
.BI \-\-mMs " integer"
.br
largest amount of mismatches in a row for part A which will not result in rejection.
.TP
.BI \-\-last_n_len " integer"
number of bases to examine to calculate the mismatch rate in the last N bases.
.TP
.BI "\-\-mM_last_n " float
highest mismatch rate for part A in the last N (specified by \-\-last_n_len) bases which will not result in rejection.
.TP
.BI "\-\-skip-anti-sense "
do not check if read could be anti-sense.
.TP
.BI "\-\-skip-reverse "
do not check if read could be reverse.
.SH AUTHORS
Matthew Martin <matthew@mttmartin.com>