Gene Expression data and variants from the same fastq raw file

Question: Gene Expression data and variants from the same fastq raw file

13 months ago by

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.

fastqc variant analysis gene expression fastq • 451 views

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modified 13 months ago by Michael Dondrup ♦ 46k • written 13 months ago by gemini.venkat • 0

We will need more informations about your projects. By fastqc you mean the fastqc program (testing reads quality etc) or fastq files ?

ADD REPLY • link written 13 months ago by Bastien Hervé ♦ 4.2k

Sorry for not being clear, I meant the fastq files.

ADD REPLY • link written 13 months ago by gemini.venkat • 0

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?

ADD REPLY • link modified 13 months ago • written 13 months ago by Bastien Hervé ♦ 4.2k

13 months ago by

JJ • 430

JJ • 430 wrote:

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.

ADD COMMENT • link written 13 months ago by JJ • 430

Would this be different if I had the fastq files for DNA-seq?!

ADD REPLY • link written 13 months ago by gemini.venkat • 0

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.

ADD REPLY • link written 13 months ago by JJ • 430

13 months ago by

gb • 780

gb • 780 wrote:

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.

ADD COMMENT • link written 13 months ago by gb • 780

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