Downloading a gene list from a sequence interval in FlyBase

This is a quick and easy way to download a list of genes that fall between an interval that you may be interested following QTL mapping, for example.

  1. First, go to FlyBase.org
  2. Under Tools, choose Genomic/Map Tools, and then choose CytoSearch.
  3. In the top option menu on the CytoSearch page, choose sequence region.
  4. Enter the sequence coordinates, but don’t forget to convert them. Your coordinates may match an earlier release of the genome. To convert, go to Tools, choose Retrieve/Convert Tools, and then choose coordinates converter. There, you can enter the coordinates you are starting with and pick the appropriate conversion. For example, if your coordinates are from release 5, you should first convert them to release 6.
  5. Back on the CytoSearch page, check all of the options you need once you have the correct coordinates.
  6. Click submit query, which redirects you to the list of genes. You could stop here if this is all you need.
  7. To download the list, click HitList Conversion Tools (at the top right above the list).
  8. A window will popup for a moment called Export Batch to Download. If you wait too long, it might disappear. Choose Genes (or whatever option you want). This redirects you to a the batch download page.
  9. Here, next to Field Data, click the format you want to download the file to. Tab-separated is a good choice.
  10. Change where you want the data exported to under the Send Results To option menu.
  11. Click Select Fields (lower right of search box).
  12. Choose the field options you want in the new page that opens.
  13. At the bottom or top of the page, click Get Field Data when you have selected all desired options.
  14. The file should download quickly and is readable in R as a .txt file.

Some things to keep in mind: FBgn numbers have changed for many genes as new information on the sequence comes available and for other reasons that are much more arbitrary. If you are looking for a way to compare the list you have just generated to a list from another study, you may need to use the FBgn aliases that are an option in step 12 to generate a look-up table of name synonyms. A good place to start for figuring out how to do that is with match() and %in% functions in R.  Also, some of the gene names for Drosophila have ‘ (apostrophes) in them and R will choke on .txt or any other type of file that has them in the data. You have to open the .txt document in an editor and remove them before reading the file into R. After this step, it R shouldn’t have a problem reading it in.

Cheers.

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Labeling panels in R

This is a brief tutorial on how to add labels to plots outside the plotting area in both basic plots and for ggplot2. I use this to label panels “A”, “B”, “C”, etc. but figuring out how to do this was surprisingly difficult. Here is my solution:

screenshot-2016-12-21-16-15-49

Here are the plots generated using the basic plot function:

screenshot-2016-12-21-16-20-05

basic plot with panels labeled “A” and “B” in R

…and the second example with basic plot. In this plot the top margin is smaller:

screenshot-2016-12-21-16-21-09

basic plot with panels labeled “A” and “B” in R

basic plot with panels labeled “A” and “B” in R

Here are the plots using ggplot2:

screenshot-2016-12-21-16-21-52

ggplot with panels labeled “A” and “B” in R

…and the vertical version:

screenshot-2016-12-21-16-22-32

ggplot with panels labeled “A” and “B” in R

If you want to tweak the exact location of the plot labels, this is easily done in ggplot2. You simply adjust the x and y values by very small increments, making sure to stay between 0 and 1.

Drumroll please!!!!!

I am inordinately self-satisfied and ridiculously excited to announce that coqui project that occupied my every waking moment as an undergraduate senior is published in the October issue of the Journal of Biogeography!!! Hooray! After cleaning up my lab space and taking a final count on all of the materials (not to mention time) spent on completing the lab work, my advisor and I sat down to write the manuscript all summer and into fall.  After being sent back to the drawing board for massive and then minor changes that included another analysis and complete concept restructuring, the paper was accepted.  The whole writing-get sent back for revisions-writing again-resubmitting process was very educational.  And kind of mind numbing at times. But we got it done!! A few people (not including my mom) have even requested copies of it!  Like I said; inordinately self-satisfied.

You can find the article here:

http://onlinelibrary.wiley.com/doi/10.1111/jbi.2013.40.issue-10/issuetoc

And, oh, by the way…that snazzy looking coqui frog on the COVER of the issue?  Yeah.  I took that. 😀

E. coqui

 

Ok, I’m done bragging now.  Back to my current research project…

Correction!

A correction is in order…In order to catch a coqui perched on a banana leaf, a few more steps are necessary.  Prior to bending the leaf to the point that you can catch the coqui, you must first bend the entire banana tree toward you.  The coqui will try to hop from its more protected spot, where it is calling from the base of the leaf so be very careful but more quickly enough that the coqui doesn’t escape.  As the coqui crawls away, farther out onto the leaf, you may then start bending the leaf to the point that you can reach and bag the frog.

 

How to Catch a Coqui Perched on a Banana Leaf (an observer’s perspective)

Dr. Klawinski had some pretty amazing catches over the last couple of weeks, and the coqui he caught that was perched on a banana leaf was one of the best.  This is what you do if you would like to make an amazing coqui catch:

Step 1:  Locate a banana tree.

Step 2:  Locate a banana leaf with a coqui on it.

Step 3:  Examine all vegetation immediately surrounding you for coquis that might be disturbed by moving toward the banana leaf with the coqui on it and catch them.

Step 4:  Decide that the banana leaf is too far away to catch the coqui (the banana tree is actually 5 feet below the immediate drop off of a bank on the side of the road—the kind they put guardrails up for).

Step 5:  Move on to other vegetation and catch the coquis that are reachable, all the while thinking about the coqui on the banana leaf.

Step 6:  2 hours later, when it is 1:30 in the morning and you only have 16 frogs so far and need 20, come back to the banana leaf, where the coqui is still perched.

Step 7:  Slowly and carefully, work your way down the 5 foot drop and edge along until you reach the banana tree.

Step 8:  Reach for the leaf, slowly bringing it down.  Try not to disturb the coqui.

Step 9:  Grab the coqui just as it is beginning to jump.

Step 10:  Bag the coqui and have someone stand on the bank, hold onto the guardrail, and pull you up.

Step 11:  Continue collecting as usual.

DNA Extractions

I am continuing to extract DNA from coqui frog feet.  I ran out of Proteinase K and had to reconstitute and dilute some new stock.  I don’t trust the accuracy of my calculations even though someone else checked them so I am extracting one sample of DNA from the Lava Trees group just to be sure it works fine.  I extracted 5 samples (because that’s how many I had Pro K for) and got some nice DNA yields.  You can see the DNA hanging from the pipette tip below.