Galaxy vs. UCSC Genome Browser Table Queries?

jnfass · 09-01-2010, 04:20 PM

Simple (heh) question ...:
What, specifically, can Galaxy do that you absolutely cannot do with the UCSC Genome Browser's Table Queries?

I'm sure that the answer is a non-empty set ... I just don't know what's in it.
Thanks,
~Joe

steven · 09-02-2010, 04:18 AM

upload and align reads?

jnfass · 09-02-2010, 11:56 AM

That's good -- I hadn't looked at their tools in a while, and it's expanded quite a bit. Thank you for prompting me to dig through the tools again.

But I was thinking more about (and should have specified) the interval operations ... you can do some complex inversion, subtraction, overlap, etc., in Table Queries, and then create custom tracks from those and then operate on those custom tracks (or am I wrong and the Table-Query-generated custom track gets replaced by subsequent queries?). Does that fully duplicate what Galaxy can do?

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09-01-2010, 04:20 PM	#1
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	Galaxy vs. UCSC Genome Browser Table Queries? Simple (heh) question ...: What, specifically, can Galaxy do that you absolutely cannot do with the UCSC Genome Browser's Table Queries? I'm sure that the answer is a non-empty set ... I just don't know what's in it. Thanks, ~Joe

09-02-2010, 04:18 AM	#2
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	upload and align reads?

09-02-2010, 11:56 AM	#3
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	That's good -- I hadn't looked at their tools in a while, and it's expanded quite a bit. Thank you for prompting me to dig through the tools again. But I was thinking more about (and should have specified) the interval operations ... you can do some complex inversion, subtraction, overlap, etc., in Table Queries, and then create custom tracks from those and then operate on those custom tracks (or am I wrong and the Table-Query-generated custom track gets replaced by subsequent queries?). Does that fully duplicate what Galaxy can do?