Here I am going to see to what degree I can identify differential splicing events that occur upon acute heat stress with the ultimate goal of determing if there is a relationship with differentiall splicing and DMLs.  [As the Tophat suite was used for RNA-seq](http://onsnetwork.org/halfshell/2015/01/08/rna-seq-tophat-via-iplant/), I will start exploring the `cuffdiff` output.  Note all output from `cuffdiff` can be [found here](http://owl.fish.washington.edu/halfshell/index.php?dir=BS-heat%2FCuffdiff2_heat-b-2014-12-20-22-27-15.4%2F). 

---

Based on the very nice documentation at <http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/> the first place I would look would be `splicing.diff`.  

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Cufflinks_1AD2D9F7.png" alt="Cufflinks_1AD2D9F7.png"/>

Having a gander at this file, there are in fact some features that appear to be significant. To make myself feel better about what I am looking at I will visualize in IGV. 

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_6_15__8_15_AM_1AD2DAAA.png" alt="Screenshot_4_6_15__8_15_AM_1AD2DAAA.png"/>

----
If my notebook holds up I should be able to refer to [this post](http://onsnetwork.org/halfshell/2015/02/26/heating-up-the-beds/) (found via IGV tag) to recreate...

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/igv___half-shell_1AD2DBDC.png" alt="igv___half-shell_1AD2DBDC.png"/>

Once IGV is open I hope to simply paste locus field (ie `scaffold1391:350297-393525` into search bar. Actually there is some [fancy formulas that would allow me to directly linkout from Excel](https://www.broadinstitute.org/software/igv/ControlIGV).

----

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/splicing_diff_1AD2DFE8.png" alt="splicing_diff_1AD2DFE8.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/splicing_diff_and_IGV_and_Fibrocystin-L_-_Google_Search_and_splicing_diff_1AD2E02E.png" alt="splicing_diff_and_IGV_and_Fibrocystin-L_-_Google_Search_and_splicing_diff_1AD2E02E.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/splicing_diff_and_IGV_and_Fibrocystin-L_-_Google_Search_and_splicing_diff_1AD2E085.png" alt="splicing_diff_and_IGV_and_Fibrocystin-L_-_Google_Search_and_splicing_diff_1AD2E085.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E0F6.png" alt="IGV_1AD2E0F6.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E13E.png" alt="IGV_1AD2E13E.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E1AC.png" alt="IGV_1AD2E1AC.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E1F6.png" alt="IGV_1AD2E1F6.png"/>

----

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E22E.png" alt="IGV_1AD2E22E.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E26F.png" alt="IGV_1AD2E26F.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E358.png" alt="IGV_1AD2E358.png"/>

---

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AD2E527.png" alt="IGV_1AD2E527.png"/>

---

So there was a good chunk and cut and pastes, some things to ponder, look at, and certainly come back to. 

Some closing help. 
That IGV session file is @ `/Users/sr320/data-genomic/tentacle/igv_session_041615.xml`
and 
Those significant splice locales

```
scaffold1391:350297-393525
scaffold1501:189-2280
scaffold1546:22946-41272
scaffold157:93056-102166
scaffold157:288396-298950
scaffold1583:636568-663717
scaffold1630:57333-61806
scaffold1643:190932-200778
scaffold1670:360106-365501
scaffold1750:71251-77856
scaffold1009:677703-719650
scaffold1009:990592-1008075
scaffold193:111771-117728
scaffold198:1032767-1055090
scaffold198:1084454-1102022
scaffold211:954418-990421
scaffold351:641567-648889
scaffold102:1297353-1322657
scaffold383:99975-117650
scaffold38366:25577-54928
scaffold1024:1037898-1043721
scaffold395:85069-105025
scaffold399:120007-128313
scaffold41228:55316-64219
scaffold41858:126164-135361
scaffold42366:124115-157800
scaffold42892:55315-57225
scaffold42904:154963-177485
scaffold43208:19552-46201
scaffold43940:65971-85144
scaffold452:65648-77493
scaffold527:16020-64639
scaffold588:178668-183438
scaffold616:53220-63262
scaffold828:110697-114691
scaffold942:369690-377892
scaffold1160:333463-390372
scaffold1213:118721-121110
scaffold128:428337-438047
scaffold1282:23471-48121
scaffold13:4222-16204
scaffold1322:265134-304245
```