Exploring the Galaxy

Let’s go day 2!

Our stuff in IPython:

https://www.dropbox.com/s/c6in770slyci8nd/Let%27s%20Go%20Day%20Two.ipynb

So to join our blastx output with the uniprot database, we used SQLshare:

SELECT * FROM [closek@gmail.com].[seastar_clc_uniprot_sprot_2.tab]blast
  Left join
  [sr320@washington.edu].[uniprot-reviewed_wGO_010714]unp
  on
  blast.Column3=unp.Entry

This gave us a new joined table :D

Specify what you want to see with

SELECT * FROM [closek@gmail.com].[seastar_clc_uniprot_sprot_2.tab]blast
  Left join
  [sr320@washington.edu].[uniprot-reviewed_wGO_010714]unp
  on
  blast.Column3=unp.Entry
  Where
  [Protein names] like ‘%interle%’

In this case it’s proteins with names like interle (interleukins?).

So now we’re looking at GO IDs…

SELECT * FROM [closek@gmail.com].[seastar_clc_uniprot_sprot_2.tab]blast
  Left join
  [sr320@washington.edu].[SPID and GO Numbers]go
  on
  blast.Column3=go.SPID

There were GO numbers in the last set, but this separates them out for easier use in the next steps and matches them to the SPIDs.

Now we’re matching the GO numbers up to GO slim terms to see the implicated processes:

SELECT * FROM [closek@gmail.com].[seastar_clc_uniprot_sprot_2.tab]blast
  Left join
  [sr320@washington.edu].[SPID and GO Numbers]go
  on
  blast.Column3=go.SPID
  Left join
  [sr320@washington.edu].[Go_to_Goslim]slim
  on
  go.GOID=slim.GO_id
  where
  aspect =‘P’  where aspect focuses on ‘P’ which represents biological processes (cellular processes = ‘C’,

Now to make a pretty plot!

Brought in the table into excel in a csv format.  Then selected all of the data and made a pivot table, which made counts of each time a GOslim term was used.  Using the chart maker, I could make a pie chart of the different processes that were represented.  Note that this does not represent the number of contigs, as there were multiple GOslim terms matched to single contigs (so we didn’t remove any duplicates).

SSTransGOslimplot_reynsattempt

OOOOOH PRETTY COLORS

 

Galaxy fun:

https://usegalaxy.org/u/ryosh/h/unnamed-history

After uploading the GOslim results onto galaxy, we could use a number of tools for exploring the data!  See the link :D

 

 

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