Posts By: Steven Roberts

Where are they now?

Posted by & filed under Cgigas DNA Methylation.

tldr In an effort to find out where heat stress induced differentially methylated loci are in the oyster genome (to ultimately inform on function) I have been using bedtools to see where the DMLs lie on the genome. As this was done on an array platform I also felt I need to take into consideration… 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

Re-defining Cgigas Canonical features

Posted by & filed under qdod.

Below is an updated version of canonical genome tracks as part of the qdod project – @ github. Updates include details on version 25 gff files and adding the TE track derived via WU-Blast. Canonical Feature Tracks (Ensembl) Ensemble provides a feature tracks that are updated on a regular basis. They can be directly accessed… Read more »

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 »