fix-trinity-output

Fix output fastq files from trinityrnaseq

Install

All systems
curl cmd.cat/fix-trinity-output.sh
Debian Debian
apt-get install ruby-fix-trinity-output
Ubuntu
apt-get install ruby-fix-trinity-output
image/svg+xml Kali Linux
apt-get install ruby-fix-trinity-output
Windows (WSL2)
sudo apt-get update sudo apt-get install ruby-fix-trinity-output
Raspbian
apt-get install ruby-fix-trinity-output
Dockerfile
dockerfile.run/fix-trinity-output

ruby-fix-trinity-output

Fix output fastq files from trinityrnaseq

trinityrnaseq outputs fastq files that have been 'corrected' Unfortunately these files are no longer properly paired and therefore can't be used in most aligners such as bowtie2 and snap-aligner. This script attempts to fix that and produce 2 properly paired fastq files and a fastq file containing single reads