Hello,
We have Illumina de novo transcriptome data of 3 different samples. We united the 3 samples and created from them contigs using different methods and united them with CAP3.
Now we want to check for differential expression in the 3 different samples using the contigs we defined. The problem is that there is redundancy in the contigs (due to either incomplete assembly or to real different transcripts from the same locus).
So it is a problem to map the reads uniquely to our contigs.
Any suggestions how to check for differential expression?
We have Illumina de novo transcriptome data of 3 different samples. We united the 3 samples and created from them contigs using different methods and united them with CAP3.
Now we want to check for differential expression in the 3 different samples using the contigs we defined. The problem is that there is redundancy in the contigs (due to either incomplete assembly or to real different transcripts from the same locus).
So it is a problem to map the reads uniquely to our contigs.
Any suggestions how to check for differential expression?
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