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alexdobin / STAR

RNA-seq aligner
MIT License
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What happens if my GTF has different entries for same locus #1915

Open AresRASP opened 1 year ago

AresRASP commented 1 year ago

Hello

Sorry if maybe it is a very trivial question: I want to create a GTF concatenating a gene GTF and a repeat GTF and use it for the indexing step. I checked that there are 414 exact same loci that exist in both geneGTF and repeatsGTF with different names in each one. If I simply concatenate both, will STAR have problems if there is two entries for the same loci?

Thank you very much. Ares

alexdobin commented 1 year ago

Hi Ares,

there should be no problem with overlapping loci. If you are using STAR read-per-gene counting options, the overlapping loci will affect the counts.