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So I am trying to change my MAXKMERLENGTH to 99....this is a straight forward thing...but for some reason when i change it at either the command line or in the makefile it stays 31. I even see the maxkmerlength=99 displayed while it compiles, but when I run velveth to see the compilation settings it still displays 31?? Anyone else experience this?
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We have successfully compiled velvet with that length set to 60 and I see references on the net where people have used numbers higher than 100.
Have you looked carefully through the compilation log to see if there was any clue about your observation. -
it looks like you have to recompile velvet for the new length you want. I have not tried this but there looks to be a goo explanation here...
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What were the exact commands used during compilation? I've changed these settings quite a few times and don't recall any issues.Comment
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Did you try
They posted the solution on BioStars here is the link,Code:make 'MAXKMERLENGTH=99'
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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Today, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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