I am analysis RNAseq data using salmon quant to get TPM value, i used the cDNA file as reference transcriptome for my bacteria (sinorhizobium meliloti strain 1021) but salmon quant does not work(378 & 400 in my shared history), i tried salmon
quant with another cDNA file and worked (356 in my shared history), but did not work with my bacteria cDNA, could you please what is the problem with this file?
i attached the link of bacteria cDNA in ENSEMBL Dataset:
Yes, we’ll need to see all of the data in place inside your history to offer specific advice. You can post the share link back here, then unshare once we are done.
This guide includes most of the technical details that we’ll be helping to review.
Some guesses: You mention the reference transcriptome, but not the reference annotation. You will want to use both at the Salmon step if the goal is to run a tool like DESeq2 after. The features in the annotation will have common identifiers with the transcriptome fasta – so be sure to check that is true and simplify the fasta > title lines as needed.
Also, most people do not need to include the reference genome at this stage. But you can share what you have and explain a bit more about your goals as we walk through some suggestions.
I would like to express my sincere gratitude to you, Jennifer
I have created a cds3.fasta file that includes the coding sequences (CDS) of both my plant and the bacteria that interact with it. My research focuses on RNA sequencing in specific organs where the plant and bacteria engage with each another. Consequently, I require a reference transcriptome that encompasses both organisms. I constructed this reference using CDS data from NCBI for both the plant and the bacteria; however, I am encountering issues with Salmon not functioning properly with this file. I have come to understand that there should be no significant difference between this file (cds3) and rna.fna as reference transcriptome files, which Salmon processes effectively with that.
Could you please clarify what might be wrong with the cds3.fasta file as a reference transcriptome? the datasets in 288 are the results from salmon using cds3.fasta.
