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I am new to working with NGS data. I want to add the information of new Sequence Reads to an existing transcriptome to possibly identify new transcripts. Does anyone have an idea of how to approach the matter? My first idea is mapping the reads to the trancriptome.
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Use Tophat and Cufflinks (Trapnell et al. Nature Protocols (2012); http://cufflinks.cbcb.umd.edu/index.html) with the annotation as a guide.
I would not trust it for differential expression of isoforms, but for assembling new transcripts it works fairly well. Only use high quality reads for the assembly and be careful to filter after the final merge.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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