---
title: "01-bowtie"
output: html_document
---


```{bash}
bb/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2-build \
/home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/data/GCF_902806645.1_cgigas_uk_roslin_v1_genomic.fa \
/home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/data/roslin.bowtie
```

```{bash}
/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 \
-x /home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/data/roslin.bowtie \
-1 /home/shared/8TB_HDD_01/sr320/ncbi/SRR12227929_1.fastq \
-2 /home/shared/8TB_HDD_01/sr320/ncbi/SRR12227929_2.fastq \
-p 40 \
--very-sensitive-local  \
-S /home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/analyses/SRR12227929.sam
```

```{bash}
/home/shared/samtools-1.12/samtools view -bS /home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/analyses/SRR12227929.sam \
| /home/shared/samtools-1.12/samtools sort -o /home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/analyses/SRR12227929.bam

/home/shared/samtools-1.12/samtools index /home/shared/8TB_HDD_01/sr320/github/nb-2022/C_gigas/analyses/SRR12227929.bam
```

