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Lesson 12 Practice

Participants can work on these practice questions on their own time as a Biowulf account or local installation of IGV is needed.

Open the bigWig files for HBR_Rep1 (HBR_Rep1_hisat2.bw) and UHR_Rep1 (UHR_Rep1_hisat2.bw). Search of the gene TEF. Does it appear to be more highly expressed in the HBR_Rep1 sample? Use "Human (hg38)" as reference.

Solution Open the HBR_Rep1_hisat2.bw and UHR_Rep1_hisat2.bw `bigWig` files. Zoom to chromosome 22. Select both `bigWig` tracks, right click and choose "Group Autoscale". Search for TEF. From the IGV view, it does appear that TEF is more highly expressed in HBR_Rep1.

How many transcript isoforms are there for TEF.

Solution Right click on the Gene track and select expand. There are 5 transcript isoforms associated with TEF, although 3 of these are predicted as the accession starts with "XM" and "XR" (see https://www.ncbi.nlm.nih.gov/books/NBK50679/).

Which of the TEF isoforms is likely to be expressed?

Solution Load the BAM files for these two samples. It appears that from the splice junctions that NM_003216.4 is expressed. Although in the HBR_Rep1 sample, reads are mapping to the first exon of NM_001145398.2.

Zoom to chromosome 22, position 41,387,655. Notice anything in the HBR_Rep1 sample?

Solution It looks like there is a heterozygous SNP, where the reference is C but some reads are showing T.