---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-09-08 19:51:15+00:00
layout: post
slug: data-received-jays-coral-epiradseq
title: Data Received - Jay's Coral epiRADseq
categories:
  - 2016
  - Miscellaneous
tags:
  - coral
  - epiRAD
  - Porites
  - RAD
  - RAD-seq
---

We received notice that [Jay's coral (Porites spp) epiRADseq](https://onsnetwork.org/jdimond/2016/08/02/rad-sequencing-days-12/) data was available from the Genomic Sequencing Laboratory at UC-Berkeley.

Downloaded the FASTQ files from the project directory to [Owl/nightingales/Porites_spp](https://owl.fish.washington.edu/nightingales/Porites_spp/):


    
    <code>time wget -r -np -nc -A "*.gz" --ask-password ftp://gslftp@gslserver.qb3.berkeley.edu/160830_100PE_HS4KB/Roberts</code>





Generated MD5 checksums for each file:


    
    <code>for i in *.gz; do md5 $i >> checksums.md5; done</code>







Calculate total number of reads for this sequencing run:


    
    <code>totalreads=0; for i in *.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$((linecount/4)); totalreads=$((readcount+totalreads)); done; echo $totalreads</code>



Total reads: 573,378,864





Calculate read counts for each file and write the data to the [readme.md](https://owl.fish.washington.edu/nightingales/Porites_spp/readme.md) file in the Owl/web/nightingales/Porites_spp directory:


    
    <code>for i in *.gz; do linecount=`gunzip -c "$i" | wc -l`; readcount=$(($linecount/4)); printf "%s\t%s\n" "$i" "$readcount" >> readme.md; done</code>





See this [Jupyter notebook](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20160314_Olurida_GBS_data_management.ipynb) for code explanations.



Added sequencing info to [Next_Gen_Seq_Library_Database (Google Sheet)(https://docs.google.com/spreadsheets/d/1r4twxfBHpWfQoznbn2dAQhgMvmlZvQqW9I2_uVZX_aU/edit?usp=sharing) and the [Nightingales Spreadsheet (Google Sheet)](https://docs.google.com/spreadsheets/d/1_XqIOPVHSBVGscnjzDSWUeRL7HUHXfaHxVzec-I-8Xk/edit?usp=sharing) and [Nightingales Fusion Table (Google Fusion Table)](https://fusiontables.google.com/DataSource?docid=13IxnqIZ_2Xpz_HE-3YcnU_egASYz9ZlA0PYIDGLN#rows:id=1).