---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-03-17 16:05:52+00:00
layout: post
slug: epinext-adaptor-1-counts-lsu-c-virginica-oil-spill-samples
title: Epinext Adaptor 1 Counts - LSU C.virginica Oil Spill Samples
categories:
  - 2015
  - LSU C.virginica Oil Spill MBD BS Sequencing
tags:
  - barcodes
  - bioinformatics
  - Crassostrea virginica
  - demultiplexing
  - Eastern oyster
  - FASTQ
  - fastx_barcode_splitter
  - grep
  - ipython notebook
  - jupyter notebook
  - LSU
  - oil
---

Before contacting the Univ. of Oregon facility for help with this sequence demultiplexing dilemma, I contacted Epigentek to find out what the other adaptor sequence that is used in the EpiNext Post-Bisulfite DNA Library Preparation Kit (Illumina). I used grep and fastx_barcode_splitter to determine how many reads (if any) contained this adaptor sequence. All analysis was performed in the embedded Jupyter (IPython) notebook embedded below.

NBviewer: [20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb](https://nbviewer.ipython.org/url/eagle.fish.washington.edu/Arabidopsis/iPythonNotebooks/20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb)

<iframe src="https://nbviewer.ipython.org/url/eagle.fish.washington.edu/Arabidopsis/iPythonNotebooks/20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb" width="100%" height="1000" scrolling="yes"></iframe>



Results:

This adaptor sequence is not present in any of the reads in the FASTQ file analyzed.
