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?
