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Questions tagged [coverage]

When referring to the coverage of a base in a reference genome, the number of reads covering that base in an alignment. When referring to the coverage of a genome in a sequencing experiment, the average number of times that a base was sequenced. = total number of sequenced bases / genome size. For example, a 100x coverage means that each base was sequenced on average 100 times. For the human genome, that would be ~ 300 Gigabases.

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Metagenomic shotgun data with internal control

For 24 human stool samples I have metagenomic shotgun reads from an Illumina platform. The reads were filtered and mapped against a bacterial species library and specific maps to species were kept and ...
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Coverage required

I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing. "coverage, c = $NL/G$ (N=number of reads, L=read length, G=genome ...
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How to take into account alternative bwa mem mapping when computing coverage

when mapping short reads with bwa mem, if a read has alternative mapping positions they are reported by bwa mem in the X0 and XA tags. Now, let's say I want to compute the coverage of my bam file. ...
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CollectHsMetrics base coverage output has overlapping targets

I am trying to get base coverage information, and am using the --PER_BASE_COVERAGE output from Picard tools to get a text file of base level coverage. However, some ...
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bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...