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.
Well, yes - first of all, you cannot infer gene expression from DNA-seq - just variants (e.g., GATK for WGS) but then variants of the complete genome (depending on your reference genome). Second, you need a different mapper e.g, bwa. STAR and HISAT2 do so-called spliced alignments.
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.
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version 2.3.6
We will need more informations about your projects. By
fastqcyou mean the fastqc program (testing reads quality etc) or fastq files ?Sorry for not being clear, I meant the fastq files.
You can use your fastq (from RNA-seq) files in gene expression studies and variant analysis studies if you have a good coverage
How Much Coverage Do We Need For An Rna-Seq Experiment?