---
title: "05-pis-annot"
output: html_document
date: "2024-11-05"
---

lets trinity up a pis file..


pull pis to klone

```{bash}
wget -r \
--no-directories --no-parent \
-P ../data/raw/pis \
-A "PSC-05*gz" https://gannet.fish.washington.edu/seashell/bu-github/project-pycno-multispecies-2023/data/raw/pis/
```



```{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 200G \
--CPU 10 \
--left ../data/raw/pis/PSC-0518_R1_001.fastq.gz \
--right ../data/raw/pis/PSC-0518_R2_001.fastq.gz \
--output ../output/05-pis-annot/trinity
```


```{bash}
fasta="../output/05-pis-annot/trinity/pis-trinity.fa"

/home/shared/ncbi-blast-2.15.0+/bin/blastx \
-query $fasta \
-db ../data/blastdb/uniprot_sprot_r2024_05 \
-out ../output/06-Go-3-species/pis_blastx_sp-raven.tab \
-evalue 1E-05 \
-num_threads 20 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
> ../output/06-Go-3-species/pis_blastx_sp-raven.out 2>&1

echo "done"
```

