GTF file preparation for ICRG

[freekvh]

Dear author,

The example code nicely shows how to generate a combined human/mouse reference fasta. In the next step I want to align my reads to this merged file using STAR. STAR prefers to also use a GTF file as input (so that it known where splice juntions are) so I was wondering, are there any examples on how to correctly merge the human and mouse GTF files so that they match the fasta files generated in the example code?

Highest regards.

[maurical]

Hi, thank you for your message!
For the GTF files, what you need to do is:

• Download the latest GTFs from Ensembl
• Convert "chr" format in mouse to "m.chr"
• Combine the two GTFs (e.g. using cat)
• Use STAR to generate index
  Hope this help

Maurizio