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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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7
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1answer
444 views

Coverage calculation: long reads (RNA-seq)

Say your aim is to calculate the coverage of an RNA-seq experiment generated with long-read sequencing (so, uneven read length). Up to now, I relied on the Lander/Waterman equation: $$C = L*N / G$$...
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1answer
128 views

How to calculate overall reference coverage with MUMmer?

Is the MUMmer suite capable of calculating reference sequence coverage statistics for all query sequences collectively? It would be possible to achieve by parsing the output of ...
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4answers
611 views

Double-counting coverage of overlapped read pairs

EDIT: I do not want to make any modifications to the mapped reads, I simply want to ignore one read in a read pair if they overlap the same region. I used samtools depth to calculate the depth of ...
6
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1answer
71 views

GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?

I'm looking for official GATK documentation (or a recent manuscript) that defines a general recommendation/requirement for sequencing depth to reliably call a heterozygous point mutation in a diploid ...
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3answers
98 views

How can I calculate coverage at single bases using a bam file?

I'm looking for a way to input a vcf or bed file (with specific base positions) and a bam file, and get the coverage at each base position (ie single base bins) using the bam file. I also want the ...
4
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2answers
162 views

Plotting coverage of annotation over collection of region

I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in ...
3
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1answer
830 views

Counts obtained by featureCounts seem much less than observed coverage

I have surprisingly low counts when running featureCounts on some (single-end) RNA-seq data mapped on C. elegans genome using ...
3
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1answer
214 views

How many reads do I need to cover the entire genome?

Suppose my genome is 3 million bases and that my reads are 100 nucleotide long. I need to know how many reads I need to cover the entire genome. I start from using the equation $C = \frac{N \cdot L}{...
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2answers
57 views

How to best detect the “peaks” in RNA-seq data that are not assigned to any gene?

I encountered that many reads from single-cell RNA seq data were lost in the analysis because not assigned to any gene (genome: galgal6). I am trying to find an approach than could give me all the "...
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1answer
54 views

How to calculate AUC in coverage graph

Is there a way to calculate the area under a curve in a coverage graph? Thank you in advance. EDIT: I'd like to calculate the AUC per strand per gene in a coverage graph. I have two wig files (...
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1answer
27 views

Total read count of shotgun affected by few highly abundant sequences

I am building statistical models to analyse output from Illumina shotgun sequencing (HiSeq 4000) on stool samples (but RNA-seq data should behave similarily). The raw counts are a statistical sample ...
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2answers
22 views

Extract mapping coverage from GTF files

I am doing paired end RNA-seq analysis. I used STAR mapper and then StringTie for getting quantification of my data. After successfully running StringTie, I got .gtf...
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1answer
49 views

How many reads do I need for hybrid assembly

I have Illumina and PacBio reads and I would like to use dbg2olc for hybrid assembly. Part of dbg2olc is SelectLongestReads which select reads that sum to ...
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1answer
21 views

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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1answer
50 views

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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1answer
24 views

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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0answers
67 views

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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0answers
113 views

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 <...