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, I will start exploring the cuffdiff output. Note all output from cuffdiff can be found here.
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.
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.
If my notebook holds up I should be able to refer to this post (found via IGV tag) to recreate…
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.
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
Should make a genome feature track of these splice differences and compare to location of DMLs
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