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.
Best wishes,
Christian
