Dear Galaxy Biostar team,
After receiving some wonderful feedback from your team I'm currently trying to figure out how to correctly order the rat rn5 genome ready to use as a custom reference genome for GATK variant analysis on the public galaxy instance. I have downloaded the rn5 genome from UCSC and have uploaded the genome via FTP to galaxy. Having converted the file to the tabular format from FASTA I believe I now need to separate the file in order to correctly order the chromosomes (chr1, chr2, chr3 .... chrX, chrY, chrM). Which particular tool should I use for this as I'm unsure what would be most appropriate. I know how to run the sorting of the individual files for these new files through Filter and sort > Sort column 1 > Alphabetical/Numerical order (depending on file) and then concatenate the files and convert back to FASTA ready for use as a custom reference genome.
Would it be possible to indicate the particular steps to complete this process please? Any information or link to further information on this would be greatly appreciated.