RNA seq analysis
I have TCGA level 3 Illumina RNA seq data...now, I need to analyse what data or information it contains.so suggest me how to analyse it with proper steps and tool.
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payaljain89 •
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Your question is too vague. What are you exactly trying to do ? Level 3 data is generally processed data with final expression estimate. Again level 3 data has expression for different subtypes e.g, exon, isoform, gene, splice junction, etc. What type of data are you dealing with RNASeqV1 or V2 ? Both are generated with different processing pipelines and dealing with them needs different approaches. You should provide more details.
it is RNAseq V1
agree, the question is too vague/ too broad. Also, there is a gazillion of questions dealing with each step of RNA-seq here, each of which more specific. See all questions under Similar posts ----------------------------> (yes, look to the right;)
it is level 3 RNASeqV1 n i want to know how to do gene quanitification?
If you have BAM files use tools like featureCounts from Subread package or HTSeq-count for quatification. I prefer featureCounts.
But it seems like you already have Level 3 data from TCGA, which is already quantified expression. If you want to do differential analysis there are 100s of tools available like DESeq, edgeR, etc.,
User http://galaxyproject.org/ -> Rna-Seq