choice of reference for transcriptome assembly

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8.3 years ago

SJ Basu ▴ 60

Hello People,

I have non-model plant transcriptome data that has to be assembled in reference based mode. Now my question is to what would be best choice as reference : cDNA or CDS

Now as I understand cDNA sequences are the transcript sequences from a gene while CDS sequences are parts of cDNA sequence (or exons). right ?? So will mapping to CDS suppose to guide the assembler better ???

PS: both cDNA and CDS is draft mode even the genome. And it has to be cDNA or CDS, cannot map it to the genome.

RNA-Seq Assembly cDNA CDS • 2.2k views

ADD COMMENT • link updated 8.2 years ago by Biostar 20 • written 8.3 years ago by SJ Basu ▴ 60

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CDS represents only protein coding genes. cDNA represents non-coding RNAs as well as non-coding parts of the protein coding genes such as UTRs. So cDNAs are spliced exons. CDSs are part of cDNAs that code for protein and are thus fraction of total exons.

ADD REPLY • link 8.3 years ago by Satyajeet Khare ★ 1.6k

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