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I am doing some experiment using BowTie and WHAM which are short read aligners that aligns short DNA sequences (reads) to the human genome. In WHAM, it is specified that for 75 bps reads, it is biologically required to allow matching with two errors and if the read length increases, allowed mismatch errors should increase. Now, I want to experiment with those two tools on 150 bps. Can anybody help me what should be the allowed matching errors for 150 bps or where can I find information about it ? Actually, I want information about, "maximum tolerated miss match errors" which is biologically relevant or for various (specially 150 bps) read length. I became confused because of this list of aligners, which has varied "maximum tolerated miss match errors". Can anybody please help me about this ? Thanks in advance.
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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...