Question: Aggregate Datapoints returns only nan
gravatar for dvc596
2.5 years ago by
dvc5960 wrote:


I just can't get Aggregate Datapoints phastCons to work. I have a bed/interval file, I set the metadata to say it's from hg18 so I can choose phastCons in the Aggregate Datapoints tool and then I run it.

But the values I get back are all "nan". Average, min, max, all "nan".

The metadata for the bed file puts the right values for the Chrom, Start, and End columns, but it also specifies the strand column. I can't tick off "strand" and it keeps saying that column 1 (which is my Chrom column) is the strand column. I don't know if it has anything to do with this (but I suppose phastCons doesn't use the strand column for anything?).

Kind Regards

ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by dvc5960

We are testing this out - more feedback very soon. Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Testing shows that when regions derived from hg18 are used, the tool reports output without a problem.

There are likely one of two issues going on with your data:

  1. There is no overlap between the intervals in your set and the target phastCons dataset. You could visualize the data at the UCSC browser for hg18 to confirm this.

  2. The intervals are from another genome build. The tool Lift-Over is able to convert coordinates between UCSC hosted human (hg17, hg18, hg19, hg38) builds.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k


I found that the problem was that I was using 3 column bed files. When I added some data to all the lines in the bed file to make it a 12 column bed file, Aggregate Datapoints with phastCons worked.

On the Aggregate Datapoints page I don't think it was very specific that it didn't accept 3 column bed files. It seemingly only requires that you specify which columns are Chrom, Start, and End.

Kind Regards

ADD REPLYlink written 2.5 years ago by dvc5960
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