Question: Encountered message from UCSC: "Reached output limit of 100000 data values"
0
gravatar for gzbyzyx
22 months ago by
gzbyzyx0
gzbyzyx0 wrote:

Hello, I am a green hand in using Galaxy. I have got two tables from UCSC, one is about the miRNAs:

Chrom Start End Name Score Strand ThickStart ThickEnd chr1 30365 30503 hsa-mir-1302-2 0 + 0 0 chr1 1167103 1167198 hsa-mir-200b 0 + 0 0 chr1 1167862 1167952 hsa-mir-200a 0 + 0 0

The other is about phastCons100way (genome):

variableStep chrom=chr1 span=1 30373 0 30374 0 30375 0 30376 0 30377 0.00785827 30378 0.0392913 30379 0.0471496

I would like to use the "Aggregate datapoints" (such as phastCons, GERP, binCons, and others for a set of genomic intervals) tool in "Operate on Genomic Intervals", and hoping to get the mean conservation score of all the miRNAs. I did get a table after processing, something like:

1 2 3 4 5 6 7 8 9 10 11 chr1 30365 30503 hsa-mir-1302-2 0 + 0 0 0.143327972588 0.0 0.974425 chr1 1167103 1167198 hsa-mir-200b 0 + 0 0 0.552092846375 0.0 1.0

But I found after the chromosome 17, data are missing:

chr17 30117078 30117172 hsa-mir-423 0 + 0 0 nan nan nan chr17 30117085 30117160 hsa-mir-3184 0 - 0 0 nan nan nan

And a warning message occur:

"Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated."

I would like to know how to deal with this problem? I have tried seperated the miRNAs table into two tables, but it doesn't work. I think maybe the "phastCons100way (genome)" table is too big to be handled?

ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by gzbyzyx0
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The UCSC table browser does not permit data transfers that exceed 100k lines. This is true whether the data is extracted into Galaxy or downloaded directly from the Table browser outside of Galaxy.

Instead, obtain the data from the UCSC Downloads area. Download locally using their instructions, FTP to Galaxy, then load into a history for use.

Best, Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k

Thanks! I will have a try.

ADD REPLYlink written 22 months ago by gzbyzyx0
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