Question: Ensembl Genome annotations versions
0
gravatar for ofonov
2.2 years ago by
ofonov0
Norway/Oslo
ofonov0 wrote:

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?

ensembl annotation genome • 808 views
ADD COMMENTlink modified 2.2 years ago by Emily_Ensembl18k • written 2.2 years ago by ofonov0
2
gravatar for Emily_Ensembl
2.2 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

The latest data is always the most up-to-date and highest quality.

ADD COMMENTlink written 2.2 years ago by Emily_Ensembl18k

Thank you for the reply. Are Ensembl annotations based on the primary assembly (e.g GRCh37), or on the patched assemblies? Are there any difference between versions of annotation, except the updated features?

ADD REPLYlink written 2.2 years ago by ofonov10

They're on the patched assemblies, which will be the difference.

ADD REPLYlink written 2.2 years ago by Emily_Ensembl18k

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?

ADD REPLYlink written 2.2 years ago by ofonov10
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