---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-09-20 00:17:30+00:00
layout: post
slug: transcriptome-alignment-olympia-oyster-trinity-transcriptome-aligned-to-genome-with-bowtie2
title: Transcriptome Alignment - Olympia oyster Trinity transcriptome aligned to genome
  with Bowtie2
categories:
  - 2018
  - Miscellaneous
tags:
  - bowtie2
  - mox
  - olympia oyster
  - Ostrea lurida
  - transcriptome
---

Progress on generating [bedgraphs from our Olympia oyster transcriptome](https://github.com/RobertsLab/resources/issues/356) continues.

[Transcriptome assembly with Trinity completed 20180919](https://robertslab.github.io/sams-notebook/posts/2018/2018-09-19-transcriptome-assembly-olympia-oyster-rnaseq-data-with-trinity/).

Next up, align transcriptome to Olympia oyster genome.

Alignment and creation of BAM files was done using Bowtie2 on our HPC Mox node.

SBATCH script file:





  * [20180919_oly_transcriptome_bowtie2.sh](https://owl.fish.washington.edu/Athaliana/20180919_oly_transcriptome_bowtie2/20180919_oly_transcriptome_bowtie2.sh)



Alignment was done using the following version of the Olympia oyster genome assembly:



  * [Olurida_v081.fa](https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa)





* * *





# RESULTS:



Output folder:





  * [20180919_oly_transcriptome_bowtie2/](https://owl.fish.washington.edu/Athaliana/20180919_oly_transcriptome_bowtie2/)



Sorted BAM file:



  * [20180919_Olurida_v081.sorted.bam](https://owl.fish.washington.edu/Athaliana/20180919_oly_transcriptome_bowtie2/20180919_Olurida_v081.sorted.bam)



Sorted & indexed BAM file (for IGV):



  * [20180919_Olurida_v081.sorted.bam.bai](https://owl.fish.washington.edu/Athaliana/20180919_oly_transcriptome_bowtie2/20180919_Olurida_v081.sorted.bam.bai)



Will get the sorted BAM file converted to a bedgraph for use in IGV.
