Part 7: Visualize gene expression in IGV

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.

Once you have installed IGV, you can open the GUI and follow the description here 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.