3.9 years ago by
Thanks for your feedbacks.
As you guessed, I'm a newbie, I've been playing with galaxy for 2 weeks, and frankly, I'm starting to loose it.
The end goal is to get a list of SNPs I can be confident with (I'm far from getting there,I'm just starting to understand how to map and filter my reads, but I'm so confused with pileup, mpileup,GATK)...
Regarding the previous post, I'm not trying to modify my fasta file into a .gff file, sorry if I was not clear. I was talking about assigning the annotation file to the fasta file. When I created my reference genome using custom build, I uploaded my fasta file ( nucleotides) and a .gff file which contains all the annotations (so that later I have information on genes and coding region ect...). When I upload my .gff file, I link it to my reference genome fasta file.
Now that I modified my fasta file, I would like my .gff file to be linked to that one instead of my initial fasta file (which had 2 line), just to be sure that I'm not loosing this database further down the track. But maybe I can specify it later when I am at the SNPs analysis stage and don't have to worry about it for now...