Thank you for your kind reply.
I am performing a RNA seq data analysis using Galaxy.
My samples are mice sample.
So the first step I have done was to upload the file> UCSC Main on Mouse: wgEncodeGencodeBasicVM25 (genome).
Then i did the Quality control of raw reads using the tool FastQC.
Subsequently I performed the Read alignment ¬ Genome based using RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.6a).
Then I perform the Quality control of aligned reads using Multi QC aggregate results from bioinformatics analyses into a single report (Galaxy Version 1.9).
After I did the Read quantification using htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file (Galaxy Version 0.9.1+galaxy1), in which In the voice Aligned SAM/BAM File> my file of interest and in the voice GFF File**>** UCSC Main on Mouse: wgEncodeGencodeBasicVM25 (genome).
Then I did the DESeq2 Determines differentially expressed features from count tables (Galaxy Version 126.96.36.199+galaxy1) .
After this I would like to perform the tool Join two Datasets side by side on a specified field (Galaxy Version 2.1.3), I have trouble in this part of the analysis. I put in the voice Join> my Deseq2 file of interest and in the voice with> the file UCSC Main on Mouse: wgEncodeGencodeBasicVM25 (genome).
But it is not right because after I perform such analysis I do not obtain for each gene for expl ENSMUST00000021332.9 the name to whom it is associated, in order to know which genes then are upregulated or downregulated.
I miss the file of UCSC Main on Mouse: wgEncodeGencodeBasicVM25 (genome) in which I have the name of the transcripts.
I hope it is clear now.
Looking forward to hearing from you.