Question: SnpEff using -onlyprotein option (meaning-Only use protein coding transcripts)
gravatar for prasundutta87
2.4 years ago by
prasundutta87330 wrote:


My aim was to get variation information/annotation about some of my genes of interest whose differential expression details I got from their RNAseq data.

Since, my variant calling tool will give information of all non-coding genes and probable unknown genes as well, I decided to annotate the variants (which were called using RNAseq reads) using SnpEff with -onlyprotein option (meaning-Only use protein coding transcripts). The reason was that, it will only annotate the variants that arose from transcripts from protein coding genes and not from anywhere else. But, I got variants annotated that were in downstream gene variant/intergenic that is not possible.

I have already asked about 'downstream gene variant/intergenic' issue in another post (, the reason about this post is if I have understood '-onlyprotein ' option wrong and if its ok to get the results I am getting.

snp rna-seq software error gene • 685 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by prasundutta87330
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