Hi everyone!
I'm new to RNA-seq and using Salmon for the first time to quantify my reads. I first need to build an index. From the documentation, I understand you have to do this using a transcriptome Fasta file. The files I have are:
GCA_000027065.2_ASM2706v1_genomic.fna
GCA_000027065.2_ASM2706v1_genomic.gff
The available files for my organism (that I can find) are as follows:
I was going to build a transcriptome using these 2 files from the above list:
Cronobacter_turicensis_z3032_gca_000027065.ASM2706v1.cdna.all.fa.gz Cronobacter_turicensis_z3032_gca_000027065.ASM2706v1.ncrna.fa.gz
My questions are: 1) Is this the best way of going about this?
2) Is the cDNA file I am using for building the index the right transcriptomic file to use?
3) Do I merge the cDNA file and a ncRNA file & use the merged file to build the index? And how do I merge these to files preserving the integrity of the files?
The rest of my code reads as follows:
For building the index: salmon index -t transcriptome.fna -i GCA_000027065.2_ASM2706v1_index
And running salmon: salmon quant -i GCA_000027065.2_ASM2706v1_index -l A -r raw/${samp}.fastq.gz -o quants/${samp}_quant
Any advice or links to further reading would be greatly appreciated!!