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Do you mind sharing information regarding the .FASTA file that you got out of nowhere as I have a .gz file and extraction results in a large number of other files. So could you tell tell us how did you manage to get a FASTA file?
I'm running a transcriptome study and my seq name columns is populated by the codes of my contgis, it's possible to run this analysis around the content of description column (which contaisn my uniprot accesion codes obtained after blastx)?? or it's mandatory to modify the seqname column to contain these codes wich I have mentioned and then perfom the test??
It is important that the names of your ID lists (test and/or reference set) are the same as the sequence name column of you annotated blast2go project. If the Id list you have are the values which appear in the description column you could use the "select by description function" in combination with the "Create ID list of Column" context menu to create the "translated" ID lists. Maybe this video might also be helpful since it shows how to create ID list from a selection: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-MWMTcgq-wEY.html
In this case, we obtained the GO annotated human genes with Ensembl IDs via BioMart as reference, so we use the Ensembl IDs as test set (see ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-HP4JfENFFPs.html). If you already have an annotated data set just make sure that your test set IDs used for the Fisher's Exact Test have the same IDs as your Blast2GO project.
