For this part of the hands-on, you need to download some data to your computer to visualize it locally. These files are:
- the contigs of you genome of interest
/work/projects/embomicrobial2020/data/metaT/binning/<SAMPLE>/<MAG>.fasta.contigs.fa- the .bed file you created in the last step
- the alignment files and their indices
/work/projects/embomicrobial2020/data/metaT/binning/<SAMPLE>/<MAG>.mt.bam,/work/projects/embomicrobial2020/data/metaT/binning/<SAMPLE>/<MAG>.mg.bam,/work/projects/embomicrobial2020/data/metaT/binning/<SAMPLE>/<MAG>.mt.bam.bai, and/work/projects/embomicrobial2020/data/metaT/binning/<SAMPLE>/<MAG>.mg.bam.bai- the filtered GFF file
/work/projects/embomicrobial2020/data/metaT/annotations/<SAMPLE>/<MAG>.annotation_CDS_RNA_hmms.gff
IGV is a graphical interface for genome visualization. You can run it on your computer. Here's how you can install it: get IGV <_static/getIGV.pdf>.
Once you have installed IGV, you can open the GUI and follow the description here <_static/runIGV.pdf> to visualize the MAG, the metagenomics and metatranscriptomics reads that map to it, the positions of the open reading frames, and the positions of the metatranscriptomics-only contigs we were able to recover in the last step.
Tasks
Explore the variation in coverage depth in the metagenome and metatranscriptome.
Focus on the metatranscriptome: can you see polycistronic operons? Compare the pattern of coverage with metatransctiptomic reads to the positions of the metatranscriptome-assembled contigs. Do you see a pattern? Can you find positions with a surprising coverage depth?
Use the search bar to find a gene with the KO annotation K00635. This is a key gene for the lipid-accumulating phenotype of Microthrix parvicella and the whole floating sludge community.