March 9, 2017
March 8, 2017
March 6, 2017
Archive
Tags
Recent Posts
February 28, 2017
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...
October 6, 2016
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,...
October 2, 2016
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...