Question: Galaxy unable to recognize MAF imported from UCSC genome browser
0
gravatar for ana16
2.0 years ago by
ana1620
ana1620 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.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by ana1620
3
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for ana16
2.0 years ago by
ana1620
ana1620 wrote:

Thanks Jen! I will try that.

ADD COMMENTlink written 2.0 years ago by ana1620
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