I have genomic SRR file (DNA-seq) for a pseudomonas genome. I used a file containing corresponding cDNA sequence and nucleotide sequence of my gene of interest to build the index by using the salmon tool. Then, used samtools to create SRR.bam file
salmon quant -p 10 -i SRR_index -l A -1 SRR_1 .fastq -2 SRR_2.fastq -z -o SRR_qt | samtools view -bs > SRR.bam samtools sort SRR.bam SRR.sorted.bam samtools index SRR.sorted.bam
Then load the .fasta files ( the index.fasta.fai was in the same directory), *.gff files of the to the IGV. I also loaded .sorted.bam file in IGV but I can't see anything.
Please give me a solution.