Dear Biostars, Hi
I have the RNA-seq data of a salmon fish (3 cond1 and 3 cond2 as biological replicate and both are paired-ends -> 12 fastq files ) and I have done Trinity de novo assembly and DEG analysis on them.
Recently the draft genome of that salmon species have been released.
I want to run a genome-guided and then DEG analysis on the same data to compare the results.
Using many helps from Biostars and @Kevin Blighe, I have selected HISAT2, StringTie approach for this purpose.
First, I created an indexed genome using:
./hisat2-build -p 6 '/home/Salmon-genome/GCF_salmon_genome.fna' ht2_base_salmon_genome
and now I have 8 *.ht2 files and want to map my reads to that reference.
Q1: Please check below mapping script I have found from here to see if it is correct for my case or not. specially I need help about paired-end data mapping. what should I write instead of sample_1.fastq in this case that I have paired-end reads?
./hisat2 -p 6 -x path/to/reference/fileName -1 path/to/fastqFile/sample_1.fastq -2 path/to/fastqFile/sample_2.fastq -S /path/to/outDir/fileName.sam &> /path/to/outDir/fileName.sam.info
Q2: can I map all my 12 files to the reference genome in one script? how? (is it by using && and repeating the script, changing fastq file names?).