How to add GFP in STAR reference?
Hello,
I wanted to ask how to add GFP to a STAR reference. I have added the GFP fasta sequence to the human fasta file. Then, I want to add the GFP to the gtf.
I was going to add the below to the end of the .gtf file. Do I need to know anything about the strand? Is there a chance I would need to use the "-" for reverse strand?
GFP unknown exon 1 580 . + . gene_id "GFP"; transcript_id "GFP"; gene_name "GFP"; gene_biotype "protein_coding";
Thank you
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Not a strict requirement as far as I remember, I think it will even except a . (dot) for the strand (== unstranded feature)
I would assume the GFP fasta is in sense format so + should be OK , that it is anti-sense is not impossible but not likely
Thank you. If I put the wrong stand will I just not get any counts for GFP?
Not even I think, it will just report that reads were counted in the opposite strand, but do check 'cus if you do really stringent counting/read-assigning they might indeed not be counted in the end result.
It may be best to include a
geneentry in addition so the file matches GTF spec.Make sure your
chromosomename for GFP in genome file matches what is in the GTF file.