How to map RNASeq data to reference genome to check T-DNA insertions?

Question

[WUSCHEL]

I used "Kallisto" to map RNASeq data to reference transcriptome and have done my analysis.

How I have a confusing outcome. Out of my 5 T-DNA knockout genotypes, two of them are showing the expressing of the gene (even higher than the WT).

These are published lines and I have already genotyped them by PCR before.

Is this because of the pseudoaligning?

How can I check this? Is there any way of mapping?

P.S. I do not believe there is cross-contamination!

I am not a bioinformatician and would appreciate it if there is a step by step detailed protocol to do this.

[Nicolas Rosewick]

Try an aligner such as STAR and then check your alignment for T-DNA on IGV.

[WUSCHEL]

Thank you Nicolas,

Even if I see this T-DNA is there by this method, can I use this Kallisto o/p data for downstream analysis?

Since Kallisto is not giving reliable information on my mutant genes? I'm confused now...

[Nicolas Rosewick]

could you post the output of kallisto for T-DNA plase ? and also could you specify which reference transcriptome you used ?

[WUSCHEL]

This is the reference: AtRTD2_19April2016.gtf. What do you mean by kallisto o/p? Which o/p ?

[Nicolas Rosewick]

The abundance estimation for T-DNA (from the abundances.tsv file from kallisto quant)