What can i do with genes that appear as NA but have statistics ?

,
2

Hi @kizzy

This prior Q&A is similar to your question: Should i change de EntrezID of my genes if it has changed in NCBI?

You could use the UCSC’s GTF annotation instead (incorporate it at the first step you incorporate the other annotation). Where to find it plus some related tips: RNA STAR error on trimmomtaic files - #6 by jennaj

Whether to keep data that doesn’t have any known annotation yet (NA) is your choice. If the research goal is to discover novel features, then you would probably want to keep those. If you are not hunting for novel features, then you can restrict the analysis to known features upstream during mapping.

HISAT2 has an option to only report hits with known features: Advanced options >> Spliced alignment options

  1. GTF file with known splice sites (input the UCSC annotation)
  2. Transcriptome assembly reporting (set to: “Report only those alignments within known transcripts”)

Hope that helps! :slight_smile: