---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-09-26 17:58:17+00:00
layout: post
slug: bedgraph-olympia-oyster-transcriptome-with-olurida_v081-genome-assembly
title: Bedgraph – Olympia oyster transcriptome with Olurida_v081 genome assembly
categories:
  - 2018
  - Miscellaneous
tags:
  - bedgraph
  - bedtools
  - IGV
  - mox
  - Olurida_v081
  - olympia oyster
  - Ostrea lurida
  - transcriptome
---

I took the sorted BAM file from [yesterday's corrected RNAseq genome alignment](https://robertslab.github.io/sams-notebook/posts/2018/2018-09-25-transcriptome-alignment-olympia-oyster-rnaseq-reads-aligned-to-genome-with-hisat2/) and converted it to a bedgraph using BEDTools genomeCoverageBed tool.

Analysis took place on our HPC Mox node.

SBATCH script file:





  * [20180926_oly_RNAseq_bedgraphs.sh](https://owl.fish.washington.edu/Athaliana/20180926_oly_RNAseq_bedgraphs/20180926_oly_RNAseq_bedgraphs.sh)





<pre><code>
    #!/bin/bash
    ## Job Name
    #SBATCH --job-name=20180926_oly_bedgraphs
    ## Allocation Definition
    #SBATCH --account=srlab
    #SBATCH --partition=srlab
    ## Resources
    ## Nodes
    #SBATCH --nodes=1
    ## Walltime (days-hours:minutes:seconds format)
    #SBATCH --time=5-00:00:00
    ## Memory per node
    #SBATCH --mem=500G
    ##turn on e-mail notification
    #SBATCH --mail-type=ALL
    #SBATCH --mail-user=samwhite@uw.edu
    ## Specify the working directory for this job
    #SBATCH --workdir=/gscratch/scrubbed/samwhite/20180926_oly_RNAseq_bedgraphs

    # Load Python Mox module for Python module availability

    module load intel-python3_2017

    # Document programs in PATH (primarily for program version ID)

    date >> system_path.log
    echo "" >> system_path.log
    echo "System PATH for $SLURM_JOB_ID" >> system_path.log
    echo "" >> system_path.log
    printf "%0.s-" {1..10} >> system_path.log
    echo ${PATH} | tr : \\n >> system_path.log

    # Set sorted transcriptome assembly bam file
    oly_transcriptome_bam=/gscratch/scrubbed/samwhite/20180925_oly_RNAseq_genome_hisat2/20180925_Olurida_v081.sorted.bam


    # Set program paths
    bedtools=/gscratch/srlab/programs/bedtools-2.27.1/bin
    samtools=/gscratch/srlab/programs/samtools-1.9/samtools


    # Create bedgraph
    ## Reports depth at each position (-bg in bedgraph format) and report regions with zero coverage (-a).
    ## Screens for portions of reads coming from exons (-split).
    ## Add genome browser track line to header of bedgraph file.
    ${bedtools}/genomeCoverageBed \
    -ibam ${oly_transcriptome_bam} \
    -bga \
    -split \
    -trackline \
    > 20180926_oly_RNAseq.bedgraph
</code></pre>





* * *





# RESULTS



Output folder:





  * [20180926_oly_RNAseq_bedgraphs/](https://owl.fish.washington.edu/Athaliana/20180926_oly_RNAseq_bedgraphs/)



Bedgraph file (1.2GB):



  * [20180926_oly_RNAseq_bedgraphs/20180926_oly_RNAseq.bedgraph](https://owl.fish.washington.edu/Athaliana/20180926_oly_RNAseq_bedgraphs/20180926_oly_RNAseq.bedgraph)



Loaded in to IGV to verify things looked OK:

![Screencap of bedgraph in IGV](https://owl.fish.washington.edu/Athaliana/20180926_oly_RNAseq_coverage_IGV.png)