I am attempting to analyze a genic locus starting from Whole genome sequencing data. I am a newbie in this field (to date I have always used specific software that provided directly to give a final result.
Now I need to analyze a specific genic sequence that I am not able to obtain with previously cited software, but I should use Galaxy (easier than linux with command line scripts).
I have fastQ files (by Illumina paired end) that I have firsly analyzed by using Trimmomatic and then align (with BWA) to a reference genome. So, I have obtained a .bam file. I am attempting to obtain the consensus fasta sequence from this file….is it possible? o I am skipped some steps???
I have been using Galaxy tools.
Thank you in advance for you help