I'm working on reproducing results from a paper using my methods.

Make bwa index of Nipponbare v7:

Turns out there are some fasta formatting mistakes in the nipponbare ref...

Correct them:

 Prep the file for GATK:

 I processed the raw reads for alignment:

And aligned (o...

I'll be trimming the reads and removing the adapter sequences today.

For that ill use Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic & Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics,...

After getting all the files, the first step of analysis will be to assess the quality of the reads generated. 

FastQC is a good tool for this. I'll be generating reports for each lane separately to check for any lane bias. Also as these are paired end reads (PE) we will...