Side track with tracks

Posted by & filed under Cgigas DNA Methylation.

Today working on our paper looking at heat stress and DNA methylation I dived deeper into the array data in the search for what should be called a DMR. As a refresher we have tracks from the core that have 1.8+ fold difference (sig) and complementary tracks where there are three adjacents (3plusAdjacent). I made… Read more »

Wayback to just-MBD

Posted by & filed under Cgigas DNA Methylation.

Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective. While I am sure there are genome tracks around, I am ending up #doingitagain. In short I took the raw Solid reads, align to Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam,… Read more »

Hyper-splitting

Posted by & filed under Cgigas DNA Methylation.

With a good two weeks hands-off of the the array data it took a bit of time to get back on target. Following up from last time (per my instruction) I began to delve into how the hypomethylated versus hypermethylated DMLs played out with respect to genomic features. Still not convinced I am convoluting the… Read more »

Intersecting DMRs

Posted by & filed under Cgigas DNA Methylation.

To try to determine where the DMRs defined by three *sig.bedGraph files described here are located on genome – intersectbed was used, some steps and … Full notebook @ http://nbviewer.ipython.org/github/sr320/paper-Temp-stress/blob/authorea/ipynb/Array-feature-overlap-02.ipynb tlrs

Heating up the beds

Posted by & filed under Cgigas DNA Methylation.

tldr – RNA-seq feature tracks In an effort to better visualize the RNA-seq data from the heat shock experiment all accepted_hits.bam files from tophat2 analysis of the 6 libraries (3 pre, 3 post) were converted to bedgraphs. As per IGV recommendations, files were further converted to .tdf files. I tried to do this at the… Read more »

Differential Methylation in the Kitchen

Posted by & filed under Cgigas DNA Methylation.

Finally re-getting around to examing our MBD-array data in the context of RNA-seq data. Briefly we have three oysters that were heat shocked with samples taken prior to, and following. An MBD-array experiment was carried out where for each oyster we have information on 50bp genome features (selected probes on the array) whether the region… Read more »