Dear,
What kind of files should i use to "using reference genome" and where get it?
I trying to realize a SNP search in my BAM files, which is the best way?
Regards, Raphael Curvo
Tool name: Generate pileup
Tool version: 1.1.2
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/sam_pileup
Hello,
You are working on the public Main Galaxy instance at http://usegalaxy.org?
If so, choose a Reference genome from the pull-down list that is the exact same genome as used when mapping the sequences to produce the BAM alignment dataset. And if the genome is not available, you can upload a fasta version of the genome you need and use it as Custom Reference genome.
Help to determine if the genomes are a match, and for Custom Genomes:
http://wiki.galaxyproject.org/Support#Reference_genomes
http://wiki.galaxyproject.org/Support#Custom_reference_genome
If instead you are working on a local or cloud Galaxy that you administrator over, a genome can be added directly or as a Custom genome. More is in our admin help:
http://wiki.galaxyproject.org/Admin/DataIntegration
Hopefully this helps, Jen, Galaxy team
Thank you Jennifer,
But i am a really newbie in that case, i used my reference and do not find a were to pull it down in the galaxy. A friend make a BAM file so i not able to do it again with a better reference. I read about some ways to get in GATK but it was unsuccessful til now. Yes i working in a cloud Galaxy. I have a BAM sorted file and stuck for while.
