Deleted:Salmon Index

Question

[myr]

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:

http://ftp.ensemblgenomes.org/pub/bacteria/release-54/fasta/bacteria_6_collection/cronobacter_turicensis_z3032_gca_000027065/

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!!