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I'm trying to get read counts for things like reference normal forward/reverse count, alternative/reference forward/reverse counts from a bam file. I've honestly read through so many forum posts and BioStar and I can't seem to find the answer. Any help would be appreciated.
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This should still work thought I have not used it recently: http://genome.sph.umich.edu/wiki/BamUtil:_validate -
I recall running into this site a bit ago. I'll give it another go. Thank you very much.
Are read counts not something typically used/had? I'm a bit of a novice in the art, but this strikes me as very important, no?Comment
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Forward and reverse counts should be 50/50. You could get counts for all the flags, and tell from that how many go each way.
That's not a common thing to worry about.
You can't get "alternate" counts from the bam. If you make a vcf, the vcf is likely to have what you want in the DP4 value
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">Comment
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After consulting with both you guys and a seasoned coworker, I've figured out what I needed I think. Thank you guys for the answers!Comment
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I need suggestion to extract the chromosome or chromosome region (e.g. chr1: 100,000,000-200,000,000) without sorting bam file. Any idea related with this would be appreciated.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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