---
title: "Process tagseq data - PSMFC mytilus byssus samples"
output: html_notebook
---




# Data Description..


table


```{bash, engine.opts='-l'}
echo $PATH
```

# Download tag-seq data
```{bash}
wget -r \
--no-directories --no-parent \
-P ../data \
-A .fastq.gz https://gannet.fish.washington.edu/panopea/PSMFC-mytilus-byssus-pilot/20220405-tagseq/ \
--no-check-certificate

```

# unzip .fastq.gz files
```{bash}

gunzip ../data/*.fastq.gz

```


# get transcriptome

```{r, engine='bash'}
cd ../data
curl -O https://owl.fish.washington.edu/halfshell/genomic-databank/Mtros-hq_transcripts.fasta
```




# Create indices for transcriptome with Kallisto
```{bash}
# Build index
/home/shared/kallisto/kallisto \
index -i ../data/Mtros-hq_transcripts.index \
../data/Mtros-hq_transcripts.fasta
  

```

# Quantify indices with Kallisto
```{bash}
# Quantify indices
/home/shared/kallisto/kallisto quant \
-i ../data/Mtros-hq_transcripts.index \
--single \
-l 40 \
-s 1 \
-o ../output/02/ \
-t 40 \
../data/*.fastq.gz \
2>&1 | tee ../output/02/out.txt

```


