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How to extract unmapped region from reference sequence from SAM/BAM file.?
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Hi,
you can use the function coverageBed included in the bedtools suite and then, (for example using the Rpackage Rsamtools), it is really easy to select the uncovered region of your reference and extract the corresponding sequence... -
Hello,
Does anybody know any other way to extract unmapped regions of the reference sequence from a BAM/SAM/ACE file??Biologist and Bioinformatics at Universidad of Barcelona
Jose F. SanchezComment
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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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