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
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
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