Im very inexperienced with bioinformatics and I have a transcriptome that I am hoping to analyze. The 3 things I would like to do are find the expression of each gene, blast specific genes against the transcriptome, and I would like to have each gene of the transcriptome blasted online to find if it shares homology with any other genes. There are currently no reference transcriptomes or genomes of the organism and the only file I have is a single fasta file. I have downloaded the local blast executables for blasting specific sequences against the transcriptome, but in terms of doing expression analysis and blasting every gene in the transcriptome, Im having trouble. I have been looking into different analysis software online and found the galaxy site, but it looks like there is not much I can do with only a fasta file. It seems that most of the programs require a fastq, sam/bam, gff/gtf file so I am not sure if or how I can do any analysis with only a fasta file.
Any ideas of what software and analysis Im able to do with this fasta file? Any advice for me for this process?