Scribd
Upload
3 views

Ex Instr

Uploaded by

gpguosiuke1
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
3 views

Ex Instr

Uploaded by

gpguosiuke1
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 4

Viewing SNPs: Exercise Instructions

Click File > Open Session. Go to the folder where you downloaded
1   Initialize exercise:
the workshop data and select snps / snp_session.xml.

2   Go to first putative SNP locus: Type snp1 in the search box and click Go.
- Click & drag on alignments to put the column of red T’s between the centerlines.
3   - Right-click on alignments, and select Sort alignments by > base.

4   Does this look like a true SNP?


For more info, mouse over the red & blue
bar in the coverage track.

5   Go to next putative SNP locus: Type snp2 in the search box and click Go.
- Click & drag on alignments to position the 5 blue C’s between the centerlines.
6   - Right-click on alignments, and deselect Shade base by > quality.
+ select Color alignments by > read strand.
+ select Sort alignments by > read strand.

7   Does this look like a true SNP? Note this was not from a strand preserving library.
RNA-seq Data: Exercise Instructions
- Click View > Preferences, select the Alignments tab,
check Splice Junction Track, and click OK.
1   Initialize exercise:
- Click File > Open Session. Go to the folder where you downloaded
the workshop data and select rna / rna_session.xml.

Observe the two samples: Heart and Liver.


2   Each sample has a coverage track, splice junction track, and the RNA-seq alignments.

3   - Right click on the Genes track, and select Squished to display the isoforms.
- Zoom in to get a closer view of the first 4 exons of the gene.

Observe evidence of Note differences in the heart vs. liver samples and
4   alternative splicing: how they compare to the gene isoforms.

- Right click on the data (alignments or junction track) and select Sashimi Plot.
5   - In the track selection window that pops up, make sure both tracks are selected.

6   Sashimi Plot: The Sashimi Plot pops up in a separate window.


Note it is interactive: Zoom in / out. Pan. Right-click to set options.
Viewing structural events: Exercise Instructions
- Click File > Open Session. Go to the folder where you downloaded
1   Initialize exercise:
the workshop data and select svs / svs_session.xml.

2   Observe colorful alignments. By default color mode = By insert size and pair orientation

3   - Right-click over alignments and select Color alignments by > insert size.
Observe: changes in color.
- Right-click over alignments and select Color alignments by > pair orientation.
Observe: most of the initial colorful alignments are now lit up again.
- Right-click over alignments and select View as pairs.

Observe evidence High % of forward-forward pairs and


4   of inversion: reverse-reverse pairs at the same locus
Viewing variants: Exercise Instructions
- Click File > Open Session. Go to the folder where you downloaded
1   Initialize exercise:
the workshop data and select vcf / vcf_session.xml.

2   Observe the two data panels: Variant sites (upper panel) and Genotypes (lower panel).

3   - Type APOL1:S342G in the search box and click Go.


- Right-click over genotypes and select Display Mode > Squished.
- Right-click over genotypes and select Group By, and select attribute super_pop.
- Scroll down to see all the groups

Observe differences Variants not present in some population groups


4   between groups: and prevalent in others.

You might also like

pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy