Entering edit mode
9.8 years ago
payaljain89
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0
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.
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