Hi, I am a biochem PhD student and a new user to Galaxy. I took a “coursera” course introducing galaxy. I understand the function of galaxy and NGS pipeline of mapping SNPs into reference genome. I have two yeast genome single end sequencing data (fastq files). I am thinking mapping the SNPs between the two different strains to locate a mutation that can explain the different drug sensitivity phenotype on the plate. I am using the built-in budding yeast reference genome. I also found one reference genome in NCBI “ERX000004: Whole Genome Sequencing of Saccharomyces cerevisiae S288C”. I am starting using “FastQC”->“Map-BWA”. My final goal is to extract the SNPs data by using “VCFfliter”. I am new to Galaxy. Do you think I could finish this task alone? I found one workflow but I wasn’t able to use it because I did not have the required files for each steps in the workflow. Any advice is very appreciated. Thank you!
Yes I think you can finish this task. Please have a look at our training material about variant calling: https://training.galaxyproject.org/training-material/topics/variant-analysis/
Is has some nice examples included.
Yes, this will be possible. For your specific case - model organism genome, comparison of variants between samples - I’d recommend using the MiModD tool suite for everything after the mapping step.
There is a tutorial analysis very similar to what you are trying to achieve in the MiModD manual at:
All the tools you’ll need should be available through both usegalaxy.org and usegalaxy.eu.
To combine MiModD with bwa-mem or bowtie2 on these servers, this page:
has some useful recommendations.
Just come back here and ask further questions if you get stuck somewhere.