Hello everybody,
I´m veeeeeryyy new to the bioinfomatic tools. I want to investigate my geneexpression changes via nanopore sequencing.
Now, after running the created workflow starting with single fastq files (attached as a screenshot), I´ve resulted with UCSC ids in tabular format instead of the gene_ids I require for DESeq2. for salmon, I´ve used the Homo_sapiens.GRCh38.cDNA.all.fa file
How do I transform the files into the correct format? Did I add the wrong input? What went wrong?
It looks like you used the reference genome (chromosomes) instead of the reference transcriptome (transcripts). I also do not see your reference annotation included for the Salmon step – you will usually want to include it for the gene-transcript mapping, at the Salmon step then later for DESeq2.
The best advice I have is to get all of your reference data organized at the very start. The UseGalaxy servers will host the genome indexed, but you’ll need to supply the two other files, and UCSC hosts all of this data.
We have discussions about this, so please have a review and let us know if you have any followup questions.
