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Question: Galaxy unable to recognize MAF imported from UCSC genome browser
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gravatar for ana16
2.5 years ago by
ana16 • 20
ana16 • 20 wrote:

Hello all,

I have successfully used the "Extract MAF blocks" tool from Galaxy, using the cached alignments. However, when trying to import MAF blocks (mm9) from UCSC genome browser, Galaxy seems not to be recognizing the file. First, the number of blocks appears as: ? blocks and species are not recognized. Even trying to update metadata does not change this information. The file itself does not show signs of corruption. Any suggestions on how to solve this issue?

Thank you. Ana.
software error ucsc alignment galaxy maf • 727 views
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modified 2.5 years ago • written 2.5 years ago by ana16 • 20
3
gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Importing MAF data directly from the UCSC Table browser usually results in a partial data transfer due to the size of the files. It is possible that there is internal corruption, but it often adds in a few lines at the start of the file with a warning and that interferes with datatype/metadata assignments. Other times the file will be truncated with a message at the end (or not). In any case, there is a better, more reliable method.

Instead, locate the data in the UCSC Downloads area (under genome -> conservation) and import the data by URL from there. Or download it locally and upload to Galaxy via FTP.

Hopefully this clears things up! Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for ana16
2.5 years ago by
ana16 • 20
ana16 • 20 wrote:

Thanks Jen! I will try that.
ADD COMMENT • link written 2.5 years ago by ana16 • 20
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