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Iam working on transcriptome data from illumina genome analyzer II.I woudl like to do a velvet assembly for these short reads ,but i see lot of repeats and homopolymers like AAAAAAAAA and TTTTTTTTTTTTTTT, so i would like to know whether i should mask all the repeats before i start denovo assembly by using velvet.
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Hi ..
I am copying a reply from the velvet mailing list which I feel fits in here.
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If the absolute error length (as in the length difference between the
actual polymer and the one measured) is longer than 3bp and this error
has been observed more times than than the chosen coverage cutoff then
the error is maintained open. This is a lot of if's, so hopefully does
not occur too often.
The reason for this conservative stance on the error length is to avoid
drastic merging of genuine homopolymers (which are quite frequent). I
have not found any method to relax this constraint without having all
sorts of repeats collapse into each other.
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Best,
-Abhi
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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.Yesterday, 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... -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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