---
title: "kallisto together"
output: html_document
---

What I ran individually before

```{bash}
find /home/shared/8TB_HDD_01/sr320/ncbi/*_1.fastq \
| xargs basename -s _1.fastq | xargs -I{} /home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/{} \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/{}_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/{}_2.fastq
```


Lets do where heart, gonad, ctenedia, juvenlies and larvae are merged...


Gonad
```{bash}
/home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/gonad \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12218869_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12218869_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12226692_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12226692_2.fastq \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/gonad.out
```


processed 69,648,408 reads, 47,796,558 reads pseudoaligned



ctendia
```{bash}
/home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/ctenidia \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12218870_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12218870_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12226693_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12226693_2.fastq \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/ctenidia.out
```

juvenile (amb)
```{bash}
/home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_amb \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12207404_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12207404_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12207405_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12207405_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12227930_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12227930_2.fastq \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_amb.out
```


juvenile (sl)
```{bash}
/home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_sl \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12207406_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12207406_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12207407_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12207407_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12227931_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12227931_2.fastq \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_sl.out
```




larvae
```{bash}
/home/shared/kallisto/kallisto \
quant -i /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/data/transcriptome_v5.idx \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/larvae \
-t 40 \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12212519_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12212519_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR12227929_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR12227929_2.fastq \
/home/shared/8TB_HDD_01/sr320/ncbi/SRR8788211_1.fastq /home/shared/8TB_HDD_01/sr320/ncbi/SRR8788211_2.fastq \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/larvae.out
```



```{bash}
perl /home/shared/trinityrnaseq-v2.12.0/util/abundance_estimates_to_matrix.pl \
--est_method kallisto \
    --gene_trans_map none \
    --out_prefix /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/kallisto-0207 \
    --name_sample_by_basedir \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/heart/abundance.tsv \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/gonad/abundance.tsv \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/ctenidia/abundance.tsv \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_amb/abundance.tsv \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/juv_sl/abundance.tsv \
     /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/larvae/abundance.tsv 
```



