I am running a GATK pipeline on RNA-seq data. For the alignment I have used GATK-bunle genome - human_g1k_v37_decoy.fasta. Now I would like to use the alignment files with featurecounts to obtain TPMs, which requires a GTF annotation file. However GATK bundle does not include annotation.
Which version of the annotation should I use? Will it be OK to use the latest version of the Ensembl annotation - GRCh37 release 87? Or should I go some versions down?
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My concern was that if I used earlier version of the genome for the alignment, than the one on which the latest annotation was based, it might lead to some artefacts, since some features might have been moved due to the applied patches. Perhaps, I am overcomplicating things?
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