2.8 years ago by
At the Galaxy Main public server at http://usegalaxy.org I just ran a quick test with Stitch Gene Blocks using the default for the option Split into Gapless MAF blocks (NO). The results are as expected. Meaning that spliced and stitched fasta sequence is the output - a match for the region in the BED12.
If Extract MAF Blocks produced output, then Stitch Gene Blocks should, given the same input. Whether the BED12 file input represents a coding or non-coding transcript is not considered by the tool. If spliced regions not included in the BED12 appear to be present in the fasta output from Stitch, comparing those results to the entire region footprint, extracted as genomic sequence directly, is a good way to confirm.
All that said, your described results do not seem to be based on the same exact BED12 input (?).
If that is the case - and even if not, I suggest double checking that the region is covered by the MAF dataset (if the source is UCSC, review your region versus the Conservation track). If the region covered (by the same primary and selected genomes as used with the Stitch tool), then the MAF will have data for it. From there, confirm the input BED12 dataset formatting (and input MAF, if not using the pre-cached indexes) and that the MAF data are based on the exact same reference genome as the input BED12. This includes exact chromosome identifiers. https://wiki.galaxyproject.org/Support#Reference_genomes
If you are working on another server, the problem could be with the tool or index, even though I would expect an error for these cases, not empty results. Contacting the administrator of that instance is one option for troubleshooting, but rule out the input formatting/coverage causes for empty output first.
Hopefully this helps, Jen, Galaxy team