I am sending data from UCSC table browser to galaxy in BED format. The data is exons from a gene from the GRCh37/hg19 database. When entering the input file into extract pairwise maf blocks, the choose maf source parameter says ‘no options available.’ Why is this and what can i do about it?
Thank you.
Hi @Deuterium09,
Do you have hg18 dbkey assigned to the dataset? If you click at name of the bed file, do you see database: ? or database: hg19? If you see the former, click at Edit Attributes (pencil icon) > in the middle window find Database/Build section and in the pull-down menu select hg19.
Hope that helps.
Kind regards,
Igor
Hi @Deuterium09
have you imported alignment from UCSC, as well?
Here is an example: imported MAF blocks are in dataset #177, and interval is is dataset #3. As I have alignments in the history, the MAF source is In History (use Re-run on dataset #178 to see the job setup).
Hope it does make sense.
Kind regards,
Igor
Hi @igor and @Deuterium09
This topic has recent details about how to use the tool at ORG (or anywhere), including a history link with an example using a custom maf from the history (imported from UCSC). Note how the maf and query coordinates both have the same database metadata – that is required for this usage. Attempting to use Stitch MAF blocks tool, but lack of documentation
Maybe a server indexed maf reference is available at other servers? We dropped this at ORG. Correction: this is at ORG. The index is present but doesn’t work correctly. It did used to be based on hg19, and the AU server also used it at some point in the past, not sure about now.
Update!! ORG does have hg19 available. Screenshot of this shared history → Galaxy. I started it up to provide an example.
And the job failed. The solution is to do what @igor did and what the history in the other topic did == use a maf from the history.
