Hi,
I have Fold expression of RNAseq data obtained from Ion Proton sequencer and got the fold change data with mean in an excel sheet.
now can I analyse this fold change data using any software? there are as many as 4500 genes so manual analysis will take a lot of time.
thanks in advance
You already have fold changes. post-processing analysis is important and depends on your biological question what are you looking from it. I would recommend you to take a list of deferentially expressed genes (obtained with p-value/p-adjusted and fold change threshold etc) and proceed for pathway enrichment analysis (Over-representation or GSEA). Their are many software and platform available for these kind of analysis. Apart from this there are many other things that can be done. https://biit.cs.ut.ee/gprofiler/gost
Analysis of RNAseq data is mostly carried out in 'R' package. There are well established pipelines/packages e.g. EdgeR available in Bioconductor repository. You can use this pipeline for reads normalization and subsequent differential gene expression. contact me [email protected] for detailed pipeline/workflow.
Hello Kankona,
usually fold changes are not enough for many inferences; but anyhow, R is the obvious answer, since many packages are built to use that platform.
Best,
Roberto
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