---
title: "08-trinity-unmapped"
output: github_document
date: "2024-11-07"
author: Steven Roberts
---

```{bash}
curl -O https://gannet.fish.washington.edu/seashell/bu-github/project-pycno-multispecies-2023/output/04-pyc-hisat/PSC-0519_unmapped_reads.1.fastq
```


```{bash}
curl -O https://gannet.fish.washington.edu/seashell/bu-github/project-pycno-multispecies-2023/output/04-pyc-hisat/PSC-0519_unmapped_reads.2.fastq
```

```{bash}
export PATH=/home/shared/jellyfish-2.3.0/bin:$PATH
export PATH=/home/shared/bowtie2-2.4.4-linux-x86_64/:$PATH
export PATH=/home/shared/salmon-1.4.0_linux_x86_64/bin:$PATH
/home/shared/trinityrnaseq-v2.12.0/Trinity \
--seqType fq \
--max_memory 180G \
--CPU 30 \
--left ../output/04-pyc-hisat/PSC-0519_unmapped_reads.1.fastq \
--right ../output/04-pyc-hisat/PSC-0519_unmapped_reads.2.fastq \
--output ../output/08-trinity-unmapped
```