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I am trying to do GO analysis. However, when I run DAVID, I am getting this error:

You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type. In addition, when I am trying to add a column with gene names next to esemble ids in R in the file with differential expression genes, many genes say NA under gene name column.

I have used STAR and Salmon for the alignment,and DESEQ2 for differential expression analysis.
I have used premade indexes for both tools.
Thank you in advance!

Some of the ENSEMBL codes I used:

ENSG00000249200 ENSG00000239920 ENSG00000242295 ENSG00000235763 ENSG00000226933 ENSG00000283632 ENSG00000235838 ENSG00000232429 ENSG00000281076 ENSG00000271042 ENSG00000229119 ENSG00000253384 ENSG00000285645 ENSG00000240627 ENSG00000213590 ENSG00000270739 ENSG00000240201 ENSG00000203531 ENSG00000271626 ENSG00000250316 ENSG00000218713 ENSG00000231548 ENSG00000231049 ENSG00000286185 ENSG00000214535 ENSG00000212961 ENSG00000219747 ENSG00000259100 ENSG00000231767 ENSG00000243175 ENSG00000236804 ENSG00000240634 ENSG00000270773 ENSG00000230267

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  • $\begingroup$ Give some examples of identifiers that didn't map. Please note that many genes will lack GO annotations, though 80% feels a bit high there. $\endgroup$
    – Devon Ryan
    Oct 30 '20 at 12:20
  • $\begingroup$ ENSG00000249200ENSG00000239920 ENSG00000242295 ENSG00000235763 ENSG00000226933 ENSG00000283632 ENSG00000235838 ENSG00000232429 ENSG00000281076 ENSG00000271042 ENSG00000229119 ENSG00000253384 ENSG00000285645 ENSG00000240627 ENSG00000213590 ENSG00000270739 ENSG00000240201 ENSG00000203531 ENSG00000271626 ENSG00000250316 ENSG00000218713 ENSG00000231548 ENSG00000231049 ENSG00000286185 ENSG00000214535 ENSG00000212961 ENSG00000219747 ENSG00000259100 ENSG00000231767 ENSG00000243175 ENSG00000236804 ENSG00000240634 ENSG00000270773 ENSG00000230267 $\endgroup$
    – user9656
    Oct 30 '20 at 12:29
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DAVID last received an update in May 2016 (https://david.ncifcrf.gov/content.jsp?file=update.html), so any additions to the Gene Ontology database since then won't be present. I checked the examples you posted in Biomart and found that only 2 have GO annotations, so you're likely not missing an immense number of genes. Having said that, you'd be best served to use a more frequently updated tool than DAVID. Around 2015 there was an outcry because it hadn't been updated in 6 years and the database was so out of date that people were getting questionable results. Have a look at one of the many Bioconductor packages for convenient free solutions that are better maintained.

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  • $\begingroup$ Thank you so much for your reply!! So, there is not a problem with my index, right? I have tried gprofiler as well, but I wanted to check more tools. $\endgroup$
    – user9656
    Oct 30 '20 at 12:45
  • $\begingroup$ Your index is fine. $\endgroup$
    – Devon Ryan
    Oct 30 '20 at 12:46
  • $\begingroup$ Thank you a lot! $\endgroup$
    – user9656
    Oct 30 '20 at 12:47

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