What’s Your Problem? OpenThread

1 October, 2009 (09:00) | General Science, What's Your Problem? | By: Jennifer

wyp_q_mark2_thumbnail1 Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

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  1. Stephen Yip posted the following on October 6, 2009 at 4:52 pm.

    What is the best way to export a series of 7-bp sequence info from UCSC genome browser into EXCEL. I am looking at missense mutations from 500 genes and have created a hyperlink within EXCEL to the appropriate gene region (7 bp) within UCSC (I need to know the “context” of the mutation so will need the sequence up and downstream from the mutated basepair). So far I have been manually inputing the 7 bp sequence back into the respective genes in EXCEL. Is there a way to automate this so I don’t have to do this 500X ?

    Thanks

    Stephen

  2. Trey posted the following on October 6, 2009 at 5:29 pm.

    I’m not completely clear on what it is that would best answer this question.

    If you have a series of locations and want to download data on those locations (genes, locations, etc), you could use a combination of the table browser and Galaxy.

    1. go to the UCSC table browser and choose genome, known genes and then define the regions you want.

    2. Use selected fields output and output data fields. It comes out as a tab-delineated text file that easily opens in Excel, with all the gene information from those locations (which genes they reside in, etc).

    BUT

    Your original locations (the 7bp locations) won’t be there. You can simply add them back in using the ‘join’ function in Galaxy which will join the UCSC file to the original 7bp sequence locations mapped correctly and with data from both.

    Can you give me an example of what you have and what you want to get out of it?

    I could probably do a quick screencast of what I mean. Would make a good tip of the week :D .

    There is also this tip we did earlier on something similar:

    http://blog.openhelix.eu/?p=85

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