analysing retrieved RNAseq datasets from GEO

Question

[theaspirant]

I have retrieved different datasets (supplementary raw data as well as in SRA format) from GEO, NCBI related to particular virus. I am interested to study the differential gene expression and further downstream analysis relating with various celllular pathways. I have also retrieved the data related to miRNA. Now before performing analysis of selected datasets there are few doubt which I am not sure about.One more thing is that I will take help from my collaborator for analysis because I am new to this kind of work. But I have to set the objective for the analysis work. So I need help for setting objective here I mean what are the possibilities of analyzing retrieved data. Should I focuss on supplementary file and select some of the genes from there or start a fresh analysis again. Do I will get anything new when I will align again to same reference genome or some other (other virus strain are available). In short what can be the proper experimental design for analyzing already analyzed data after retrieving from GEO. Please excuse me if questions does not look ordered and looks fragmented, I am new to this.

Looking forward for the suggestions and possible answers thanks in advance

Answer 1

[theaspirant]

Actually I mean to say that can anybody provide some links/papers related to this..regarding objectives its vague now so not possible to write all...

[mforde84]

Related to what though? http://www.bioconductor.org/help/workflows/rnaseqGene/

Answer 2

[Daniel]

I recommend working through the RNA-seqlopedia website before going any further, to understand what is possible and what is typical in an RNAseq analysis: http://rnaseq.uoregon.edu

Answer 3

[EagleEye]

• Download SRA data as raw FASTQ file using (SRR ids can be obtained from GEO database),

  A: Downloading data from Short Read Archive

• Try following steps with the help of your collaborator,

  A: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da

Answer 4

[theaspirant]

Thanks both for the reply..!! Probably I am not clear in the question earlier, I have retrieved the SRA data and converted the same to fastq format. Since I am analyzing the already analyzed and even published data so I have to set some new objective. I have went through many literature related to my topic but unable to set new objective. I have also gone through basics of RNAseq but unable to set objective. For example If I have to study differential gene expression in virus infected and mock infected cells then what will be my new objective in similar type of data. Hope I am able to clear my questions....

[mforde84]

Honestly, if you're unsure what you want to do, then why would we know what you want to do?

[EagleEye]

It is called basis of research... yourself has to figure out what you have to/ you can do by going through the literatures (nobody knows your expertise or can read your mind) or atleast your PI/head should have some idea (you should ask this question to your PI).