Anyone have an expert opinion to share on the pros and cons of using CLC Genomics Workbench for de novo transcriptome assembly from 454 and Illumina paired end reads and mapping of Illumina reads to the assembly for digital expression values? I know that CLC uses RPKM (reads per kilobase of transcript per million mapped reads), which is not advantageous over FPKM, due to the potential for skewed data resulting from poor quality in read pairs. Any advice/opinions would be great.
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Originally posted by JQH View PostAnyone have an expert opinion to share on the pros and cons of using CLC Genomics Workbench for de novo transcriptome assembly from 454
A "con" surely is, that CLC remains a black box, you can't really tell what it does in detail.
Originally posted by JQH View Postand mapping of Illumina reads to the assembly for digital expression values?
Cheers,
Simon
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