Hi!
I`ve downloaded the "Supplementary_files_format_and_content" of one deposited dataset from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129718 ). The excel file includes RPKM values, genes and annotation for each Sample. I am not interested in re-analyzing everything from scratch but I would like just to see the trend (either UP or DOWN regulation) of specific genes I am interested. My plan then was to convert the gene_id column into gene_symbol column so it would be easier for me to identify my gene of interest but I have noticed that a lot of gene has multiple transcript_id for the same gene (and ensembl id). How am I supposed to deal with this multiple "transcript_id"? which one am I suppose to look at?
I can have for example same gene_id (ENSMUSG00000028943), same locus (4:152120313-152152454) but different length (1375, 1593 etc) and different transcript_id (ENSMUST00000105657, ENSMUST00000105656). the transcrpt_id a lots of them for multiple genes (not only 2 as shown brefly above)!
Thank you in advance!
Camilla
Marisol Herrera-Rivero thank you very much for the help! Now it`s much more clear!
Do you think that doing the average of all transcripts for that specific gene is a correct/allowed approach or the best way is to keep all transcripts per gene separated?
Hi! thank you very much! I will follow your suggestion (indeed it just to see whether some gene have a specific trend in agreement with my RNAseq data and hypothesis)!
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