data analysis
Hi Simone,
We have just received the sequencing result using smart-seq2. The input material for each sample is 10 cells and we got around 10M PE100 reads for each sample. We then tried to analysis the data using TopHat-cuffdiff workflow. The mapping rate is around 80% which is quite good. However, there are too many ( more than 8000 genes) showed differential expression. It looks like lots of genes only have expression in one sample but zero rpkm in another one. I wonder whether this is normal for this kind of experiment and how can I make sense of the gene list. Thanks for the help.
Jason
Hi Simone,
We have just received the sequencing result using smart-seq2. The input material for each sample is 10 cells and we got around 10M PE100 reads for each sample. We then tried to analysis the data using TopHat-cuffdiff workflow. The mapping rate is around 80% which is quite good. However, there are too many ( more than 8000 genes) showed differential expression. It looks like lots of genes only have expression in one sample but zero rpkm in another one. I wonder whether this is normal for this kind of experiment and how can I make sense of the gene list. Thanks for the help.
Jason
Originally posted by Simone78
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