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Old 01-20-2009, 04:37 PM   #1
foram
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Default Fraction of reads incorporated in Velvet assemblies

I was wondering what % of reads others are finding incorporated into velvet assemblies? I often see as low as 25-30% -- even with PE data, good (summary) quality scores, and high initial coverage. Is there an interpretation / reason for low % read incorporation?

I am using Illumina GA2 with reads from 45 - 76 bp and inserts from 300-600.
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Old 02-04-2009, 05:36 PM   #2
Torst
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foram,
What velvetg parameters are you using?
What method did you use to determine only 30% of the reads were used?
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Old 02-04-2009, 06:29 PM   #3
foram
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Hi Torst,

an error on my part. we are seeing 75%+ in assemblies.

thanks.
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Old 02-04-2009, 06:36 PM   #4
Torst
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What velvetg parameters did you use?

Any use of coverage cutoffs, minimum contig lengths, insert distance tolerance parameters, etc. will throw away data at varying stages.
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