Overview:

Learning Objectives:

Tutorial Running Breseq on SSCS and Trimmed Reads:

The following reference files should be copied from the $BI/gva_course/mixed_population directory into your reference folder: 1400flanking.gff3, and REL606.maksed.gff3.

cp $BI/gva_course/mixed_population/*.gff3 reference

Just like the previous tutorial if these commands are run on an idev shell they should be run in the background so both comparisons can be run at the same time. Alternatively they can be submitted to the que outside of an idev shell.

In this case we are going to be running breseq in both polymorphism mode, and targeted sequencing mode. We will also be using 2 different reference files, 1400flanking.gff3 should be used as a standard reference while REL606.masked.gff3 should be used as a junction only reference. Also we want to make good use of the 12 processors we have available so 6 processors should be used for each sample.

breseq -p -t -j 6 -o SSCS_output/trimmed -r reference/1400flanking.gff3 -s reference/REL606.masked.gff3 trimmed_1.fastq trimmed_2.fastq >& Logs/trimmed.log.txt
breseq -p -t -j 6 -o SSCS_output/SSCS -r reference/1400flanking.gff3 -s reference/REL606.masked.gff3 DED110_SSCS.fastq >& Logs/SSCS.log.txt

Again, just like the previous tutorial we now want to create a comparison file using "gdtools compare" so we can see the difference of having the trimmed reads vs the SSCS reads. This time you want to create a file "trimmed_vs_SSCS.html".

gdtools compare -h

gdtools compare -o trimmed_vs_SSCS.html -r reference/REL606.masked.gff3 -r reference/1400flanking.gff3 SSCS_output/SSCS/output/output.gd SSCS_output/trimmed/output/output.gd

The comparison table as well as the output for the trimmed and SSCS reads can now be exported to your local computer for viewing. If you are using a unix (ie mac) operating system you can use the information given in one of the previous tutorials. If you are trying to view these files on a PC (ie classroom desktop) then you will actually need to transfer the entire folder using the sftp client. To do so use the sftp client ("filezilla") and log in using the same information you use to log into tacc through putty, then navigate to where you ran this data on scratch.