What to do with genes that appear as NA but have statistics
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22 days ago
kizzy ▴ 10

Hi I'm doing an RNA-seq analysis and I'm having problems identifying some of the genes in the output of the DESeq2 tool because the list of genes obtained are in Entrez id, for context the pipeline used was Fastp > HISAT2 > feature counts > DESeq2. I used g: profiler and annotateMyIDs to identify the genes by the Entrez id, but there are still some that appear as NA in the list, so I tried to identify them manually by searching the Entrez id in NCBI and then took the coordinates from there and looking if there was a match in my samples using the visualizer UCSC and IGB, in parallel some of the genes in NCBI appears as updated and have another Entrez id associated to a gene, that gene is already identified in the list that I have, the question is can I keep the gene that is so far in the list and discard the obsolete one that had been updated?. Other than that can I discard the ones that haven't been updated and remains as NA?

featurecount DESeq2 galaxy genename entrezid • 101 views
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