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Hello! Can anybody let me know, how can I get coverage data of a single gene from BAM file. Thanks.
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Where contig is the name of the chromosome, 12 is the start position of your gene and 1000 is the end position.Code:samtools depth -r contig:12-1000 single.bam
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Use BedTools -- coverageBed should be the program you want.
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Actually TiborNagy's method is easier for a single gene. Give that a try first.
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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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