Combining RAD Tag libraries from different Illumina runs

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Table of Contents

Dec. 29, 2012 
Comparing Trachemys Stacks results between the Nov and Dec 2012 Harvard Illumina runs

    The first Illumina run of 93 Trachemys samples in Nov. shared a single HiSeq lane with many other samples(fish and flies) and resulted in
    very low coverage. Fortunately, Anna saved portions of the libraries at several stages of the RAD tag library contruction.
    In Dec. we sent a sample saved after the Pippen size selection stage to Harvard to be run alone on a single HiSeq lane.
    Almost all of the Dec. samples had twice the number of reads from Nov.
    
    While there were many more reads from the Dec run, the '-m 5' resulted in fewer total stacks than in the Nov. run (1,009,172 vs. 739,115),
    but when the data is filtered by various criteria; the Dec. run always returns more stacks and with deeper coverage (double digit vs. single digit).
Dec. 30, 2012 
Combining the Dec. & Nov. Harvard Illumina data
    
    I created a new Stacks project directory "Harvard_merged" and wrote a bash loop script that would combine the illumina samples from the Nov. and Dec. runs.
#! /bin/bash

clear

echo "starting script"

topdir=/data/simison/Analyses/Rad_tag/Harvard_merged/samples
dir1=/data/simison/Analyses/Rad_tag/Harvard_Dec_2012/samples
dir2=/data/simison/Analyses/Rad_tag/Harvard_2012/samples

for f in $dir1/*.fq_1
do
    outf=$topdir/`basename $f`
    echo $outf
    cat $f $dir2/`basename $f` > $outf
done
    I made two .sh files, one each for the foward (*.fq_1) and reverse (*.fq_2) reads and saved them to the /opt dir.
    I also made sure the files were executable: 
$ chmod 755 Cat_merge_fq1.sh
 To run the scripts, simply enter the name of the file and hit return: 
$ /opt/Cat_merge_fq1.sh
Dec. 31, 2012 
Stacks denovo_map.pl run on merged data
    
    With the additional reads, I was able to increase the filtering stringency during the Stacks denovo_map.pl:
$ nice -n 19 denovo_map.pl -m 5 -M 3 -T 16 -B TrachDec92_radtags -b 1 -t -a 2012-29-12 -D "New samples
    from Harvard Dec. 2012" -o ./stacks -p ./samples/ven_M233245.fq_1 ...
 Notice that I increased '-m' option from 3 to 5 ('-m' specifies a minimum number of identical, raw reads required to create a stack).