.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH FIX-TRINITY-OUTPUT "1" "February 2019" "fix-trinity-output 1.0.0" "User Commands"
.SH NAME
fix-trinity-output \- Fix output fastq files from Trinity
.SH DESCRIPTION
.PP
Trinity outputs fastq files that have been 'corrected'
.PP
Unfortunately these files are no longer properly paired and therefore
can't be used in most aligners such as bowtie2 and snap
.PP
This script attempts to fix that and produce 2 properly paired fastq
files and a fastq file containing single reads
.SH OPTIONS
.TP
\fB\-\-left\fR, \fB\-l\fR <s>:
fastq file of left reads
.TP
\fB\-\-right\fR, \fB\-r\fR <s>:
fastq file of right reads
.TP
\fB\-\-output\fR, \fB\-o\fR <s>:
output prefix
.TP
\fB\-\-help\fR, \fB\-h\fR:
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