Dear all, I want to count the reasds from RNA seq by using SALMON tool. I was told that the first thing to do is to create a fasta file with the sequence information (fasta file from reference genome + annotation file.GTF) such as :
(salmon) [@ws7910 RNAseq]$ gffread -w transcripts.fa -g Homo_sapiens.GRCh38.cdna.all.fa Homo_sapiens.GRCh37.75.gtf
I get this result
No fasta index found for Homo_sapiens.GRCh38.cdna.all.fa. Rebuilding, please wait.. Fasta index rebuilt. Error creating file: annotation/transcript/transcripts.fa
it creates a file named Homo_sapiens.GRCh38.cdna.all.fa.fai
On the salmon website seems that this step is not necessary so can you please tell me what am I doing wrong? and what is the best way to start using salmon?
I'd prefer to do the counting with BAM files already alignes using TopHat2