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No problem, good luck with your further analysis.
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bowtie-build error
Hi boetsie,Originally posted by boetsie View Post
SSPACE must be very useful tool for scaffolding. But when I tried to use it, the process was failed by bowtie-build step. I only have contig file contains all name with super_contig sequences without other information and there are lots of 'N' gaps between. Do I need to modify some information and get bowtie-build works? If not, what's the problem?
The reads I have are 100PE
so the library is like
lib1 ***1.fastq ***2.fastq 200 0.7 0
or I should replace 200 to 400?Comment
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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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