Question: Does GRCh38 reference genome contain 18S and 28S rRNA sequences?
gravatar for zhangzhenyusz
3.3 years ago by
zhangzhenyusz20 wrote:

Hi everybody,

I'm using STAR to analyse RNA-seq data. I used GRCh38 as reference genome and also the annotation file from ensembl site under same build. The result from STAR shows a high percentage no_feature alignments which are those aligned to reference genome but not annotated. I know 18S and 28S are not annotated in the gtf file and I wonder if the reference genome contain those sequences. Because if it contains, then the no_feature may be due to failed rRNA depletion.

Thank you!

rna-seq alignment genome • 2.6k views
ADD COMMENTlink modified 3.3 years ago by genomax92k • written 3.3 years ago by zhangzhenyusz20

Get the human rDNA repeat here: C: Removing rRNA and tRNA sequences using GTF files and align your data to it.

ADD REPLYlink written 3.3 years ago by genomax92k
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