I have worked done De Novo assembly to build a transcriptome file "Phormia_de_novo_transcriptome_assembly_V1.fasta". If I would like to assess the quality by mapping the raw read "00_fastq.txt" to my assembly file "Phormia_de_novo_transcriptome_assembly_V1.fasta". I know the first thing is to build the index, which I have tried
salmon index -t /Users/maysonlin/Downloads/De_Novo/Phormia_de_novo_transcriptome_assembly_V1.fa -i /Users/maysonlin/Downloads/De_Novo/Phormia_de_novo_transcriptome_assembly_V1.index -- type quasi -k 31 , I also looked up for some Youtube videos, so far didn't get anywhere, I have been stuck for many days. Does the assembly file and raw read file have to be in the same folder in Salmon files? What command line should I build? Please let me know, I sincerely appreciate it!