Need help inserting a custom gene sequence into ref genome and GTF file

Question

[maxwellb]

Title about says it all. I have an eCFP sequence, the transcripts for which I would like to be able to detect in my sequencing study. I have the Mm ref genome, corresponding GTF file and separately, the full sequence for eCFP. I'm just... not sure how to to insert the sequence into my ref genome and correspondingly, note it in the GTF file. Thanks!

[WouterDeCoster]

I'm not sure if I understand entirely. Do you know where the eCFP fragment belongs in your genome, i.e. the genomic coordinates?

Answer 1

[maxwellb]

Ok. It looks like this properly addresses my question: https://groups.google.com/forum/#!msg/rna-star/FGQRotrCB1Q/oQ2annphCQAJ

Answer 2

[Kristoffer Vitting-Seerup]

You just have to generate a fasta file and a GTF file with the information for eCFP and then concatenate it with the fasta and GTF file for the genome. Afterwards you need to rebuild indexes for mapping etc.

[maxwellb]

Hi Kristoffer, thanks for your reply. What tools would you suggest to do this? I'm pretty competent with shell commands and scripting etc.