Making the genome indics using different GTF files

alexdobin / STAR

RNA-seq aligner

MIT License

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Making the genome indics using different GTF files #1079

Open StephenLi55 opened 3 years ago

StephenLi55 commented 3 years ago

Hi Alex,

I made my genome indics using an older GTF file back in last year. Since then the GTF file has been updated with several changes. Just wondering would that make much difference to the alignment results? Is it worth repeating last year's analysis using the updated GTF file?

best wishes,

Stephen

alexdobin commented 3 years ago

Hi Stephen,

it will affect the results in places where the GTF was changed: if there are new splice junctions, the reads mapping to them may be affected, if there are new genes/transcripts, counting with --quantMode will be affected.

Cheers Alex