I am a total beginner in gene expression studies and variant analysis studies, I was wondering if the same raw fastqc files can be used for both studies? Or are there different fastqc files for different studies. I am working on RNAdeepseq files.
I am not quite sure about your question as there is not much information here. But maybe this helps: If you have RNA-seq fastq files (e.g., samples from 2 conditions) you can feed them after mapping (e.g., with STAR or HISAT2) into differential expression analysis (e.g., stringtie & ballgown or featureCount & limma) as well as into a variant analysis pipeline such GATK (for RNA-seq data). Note that you obviously can only call variants in the transcribed regions.
yes you can, the file format does not matter. If you do not have a reference genome you can do a denovo assembly with for example the tool trinity. After that you can compare those assembly's to find SNPs. For expression analysis you can map the reads back to your assembly and use tools that are mentioned before. I think you can also use bowtie for that because in this case you dont have to worry about splice sites.