I am trying to extract multiple alignments for a large number of zebrafish regions (~90,000) to 4 other fish species using Stitch MAF Blocks. I'm giving it an interval file containing the chromosome, start, stop, and strand (all from zebrafish assembly danRer7) for these regions, but the output fasta it gives me is mostly empty.
Plugging the same chromosome/coordinates into another multiple alignment program (i.e. CodAlignView) gives me hits for some of the missing regions, so I am fairly sure there should be something there, however, CodAlignView is not high throughput like Galaxy. I am wondering if I am just using the wrong tools or if my input file is not being interpreted correctly or something. Any help would be greatly appreciated.