---
title: "01-kallisto"
output: html_document
---

```{bash}
pwd
```

```{bash}
/home/shared/kallisto/kallisto
```

```{bash}
cd ../data
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa
```




```{bash}
/home/shared/kallisto/kallisto \
index -i \
../data/cgigas_uk_roslin_v1_genomic-mito.index \
../data/cgigas_uk_roslin_v1_genomic-mito.fa
```
```{bash}

find ../data/*fastq.gz \
| xargs basename -s _L001_R1_001.fastq.gz | xargs -I{} home/shared/kallisto/kallisto \
quant -i ../data/cgigas_uk_roslin_v1_genomic-mito.index \
-o ../output/kallisto_01/ \
-t 40 \
../data/{}_L001_R1_001.fastq.gz
```