workflow question - problems with gene annotation

Question

[lessismore]

Workflow question:

Im trying to clone a gene. While amplifying it, i had some problems. I then realized that its gene model changes across genome versions meaning that i have the 5' region in the CDS that displays some indels. I have multiple transcripts in both genome versions and i realized i dont know anymore what transcript im working with because of this problem. So what workflow do you suggest? i was thinking to simply remap all reads i have from several RNAseq studies against both genome versions with some mapping tools like Bowtie or STAR and then analyse the coverage in that specific region. Ideally i could also extract the mapping reads a perform a denovo assembly, correct?

What else do you suggest OR what would you prefer?

thanks in advance

Answer 1

[colindaven]

• if de novo use all reads
• if mapping go for STAR, not bowtie2, to map splice sites accurately
• following de novo mapping to genomes using gmap is highly useful

Good luck