I want to perform RNA-Seq data analysis for DEG's, by taking RAW reads from the NCBI-SRA database, of DENV1, DENV2, DENV3, DENV4. I want to perform this analysis on a galaxy web server. I'm a bit confused about the datasets from SRA. My confusion is, in this accession no from GEO-database- GSE69602, there is a total of 116 data are present. and I took only Total cell lysate data. In total cell lysate, there are two biological replicates at each time interval, like 6hr, 12hr, 24hr, 48hr, 72hr, and the other one is mock. I performed one analysis by taking two biological replicates of 72 hr and two mocks. workflow is, FastQC-Trimmomatic-RNA-STAR, StringTie, DEseq2. I want to know that is the right way or I'm doing anything wrong & if I have to take all the data from the respective time intervals, what is the protocol to specify those data at DEseq2?
All datas are singel-end data,
if you need to see my galaxy history I can share it with you.
A big thank you in advance
I believe it would be more appropriate to construct the DESeq2 object with all timepoints and biological replicates and then specify the groups to compare using the contrast parameter in the results() function. It is well-documented in the DESeq2 vignette and in several posts on biostars.
Hi, The workflow created by you is correct you can also try EdgeR for Differential expression.
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