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  • Minimum contig & Coverage

    Hello,

    I have some 454 sequences reads from a cDNA library for a novel organism (non-sequenced genome).

    I have processed the data with CLC Genomics Workbench and done four different de_novo assemblies with 200 bp, 300 bp, 400 bp and 500 bp minimal contig length. As one would expect, increasing the minimum contig length decreases the total number of contigs (or assembled cDNAs).

    I have two questions:

    1) Is there any consensus on the minimum contig length for cDNAs?

    2) What is considered a minimal amount of coverage for any given cDNA within the final assembled contigs (cDNAs)? I would assume that rare cDNAs would have much lower coverage than abundant cDNAs.

    Thanks,
    CH
    Last edited by cement_head; 08-23-2012, 05:03 AM. Reason: clarity

  • #2
    Originally posted by cement_head View Post
    1) Is there any consensus on the minimum contig length for cDNAs?
    No. But if you throw away contigs > 500bp say, then you won't discover any transcripts that are <= 500 bp.

    2) What is considered a minimal amount of coverage for any given cDNA within the final assembled contigs (cDNAs)?
    Same as for genomic DNA. That is, there is no hard rule. 1x is probably too low. 100x is probably overkill. Somewhere in between is a reasonable trade-off between getting long transcripts, and not getting false positives.

    I would assume that rare cDNAs would have much lower coverage than abundant cDNAs.
    Yes. The assumption is the #reads is proportional to the #templates in the library.

    Comment


    • #3
      Thanks - this is what I suspected.

      Regards,
      CH

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