I was using the GALAXY project (https://usegalaxy.org/) online server, the section is Fetch alignments -- > stitch Gene Blocks, and I wanted to extract some CDS genes in drosophila maf genome alignment file (from UCSC dm6 multiz27 way maf) according to a custom made BED file converted from GFF (the original file is from flybase dmel-all-r6.07.gff) file, however, as I do the extraction, the gene sequences I get are all in '-------'. As there is no genome build for dm6 in drosophila melanogaster, I build it myself via UCSC genome browser using the dm6 fasta genome sequences. Can anyone help me to sort out this problem? Thanks!
It is unclear how a custom reference genome (fasta format) would be used with this tool.
It might be best to send in a shared history link and we can examine the inputs and processing. Paste the link, the problematic dataset numbers, and a link to this post in an email to firstname.lastname@example.org
Thanks, Jen, Galaxy Team