Investigate: Distinguish F3H-OX3 from VF36 samples

Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)

It was easy to identify which samples were ARE and not VF36 or F3H-OX3.

We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue.

To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not.

Previously, we have found that the plant selective marker gene was expressed in soybean seeds in a transgenic line.

For this task, we'll investigate whether we can use the F3H-OX3 line's plant selection marker gene to distinguish transgenic from non-transgenic lines.

See:

• Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z
• Code repository: https://bitbucket.org/lorainelab/soyseq

Maarten has sent us three files with the construct information in them. These are added to the git repository here:

• ExternalDataSets/pK7WG2-F3H.fa
• ExternalDataSets/pK7WG2-F3H.gb

In this experiment, the plant selection gene was a kanamycin resistance gene.

For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene.

To do this, we need to investigate the different tools that might be available for this task.

Let's try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence.