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!
If you specifically need help to do this on Galaxy then I suggest you post this on Galaxy help forum.
I used galaxy and mapped the reads to the yeast reference genome and obtained two BAM files for two fastq data (single-end sequencing). Am I even close to mapping the SNPs? Thank you!
You have started down the path. Here are some tutorials to consider for galaxy on this topic.