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Does anyone have decent strategy for taking isotigs.fna (cDNA sequences) and outputting a list of non-redundant isotigs that could be used for mapping rnaseq reads for differential expression analysis. I suspect I am losing about 50% of my illumina reads during mapping because they do not map uniquely.
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I guess one option would be to assemble illumina and 454 together in newbler with the -rip option and then to parse the ACE file. However I have ~90 million 100-bp HiSeq reads and so a hybrid assembly isn't possible on our hardware.
Apologies I just realised -rip doesn't work in cDNA mode. -
I heard somebody using CAP3 with the assembled isotigs as input and a single transcript (variant) per gene as output. But, you will anyways get splice variants. Aren't there any programs out there to map RNAseq reads that take splice variants in the reference into account?Comment
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