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
Monthly Archives:: February 2015
Re-defining Cgigas Canonical features
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 »
TWIF 76: Lab Meeting – February 23
Heating up the beds
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 »
Scaling BAMs down to size
TWIF 75: Lab Meeting – February 17
caption width= 1167 align= alignnone Sashimi caption
Created a gtf based on Cuffdiff gene expression…
Created a gtf based on Cuffdiff gene expression output. Available @ http://owl.fish.washington.edu/halfshell/bu-data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf
Differential Methylation in the Kitchen
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 »
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