Question: RNA seq analysis
0
gravatar for payaljain89
4.2 years ago by
India
payaljain890 wrote:

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.

rna-seq R • 1.4k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by payaljain890
2

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.

ADD REPLYlink written 4.2 years ago by poisonAlien2.8k

it is RNAseq V1

ADD REPLYlink written 4.2 years ago by payaljain890

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;)

ADD REPLYlink written 4.2 years ago by Michael Dondrup46k

User http://galaxyproject.org/  -> Rna-Seq

ADD REPLYlink written 4.2 years ago by gaurav.singh10
0
gravatar for payaljain89
4.2 years ago by
India
payaljain890 wrote:

it is level 3 RNASeqV1 n i want to know how to do gene quanitification?

ADD COMMENTlink written 4.2 years ago by payaljain890
If you have BAM files use tools like featureCounts from Subread package or HTSeq-count for quatification. I prefer featureCounts. http://subread.sourceforge.net 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.,
ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by EagleEye6.2k
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