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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Is it possible to, all in memory without writing a file, given a list of AlignedSegments and a bam header, build a bam, index and get coverage?
My current job is rate-limited chiefly by the IO overhead of writing reads to their corresponding bam files (they are split up by both cell barcode and contig). The only reason I need to write these ...
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How come bigWigSummary shows coverage greater than 1 for some region of the genome?
I am running this command, using the UCSC utilities:
bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1
to get phastCons77way ...
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How can I calculate the coverage of a gene in exome sequencing / calculate coverage per gene?
I have a bam file of whole exome human data. I now want to check coverage of a list of genes in my data. Basically, I want to get output like, for example:
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Problems with BED format for ClinCNV
I have some problems with ClinCNV(https://github.com/imgag/ClinCNV):
I made a BED file from a BAM, then i made a GC count with ngs-bits (link: https://github.com/imgag/ngs-bits )
The main idea of ...
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What should GC coverage bias plot of exome data look like?
I want to see if there is any GC coverage bias in some paired-end Illumina human exome data. Update This is for a variant calling project. I used the ...
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What are the columns in bedtools coverage output hist file?
I am using bedtools to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what ...
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Does it make sense to compare the mean relative coverages for contigs / MAGs from samples that were not co-assembled?
I have a subset of high-quality MAGs from different environments, sequenced on different runs. I want to know, for any particular MAG, if it (or something similar to it) is present in any particular ...
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Understanding exercise on file coverage with question on summary statistics
I'm doing an exercise that asks for two files:
Input 1: A target file (.bed format) contains multiple regions from
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How do you set the coverage in PacBio's Sequel II?
I am reading the Whole Genome Sequencing for de novo Assembly Best Practices
Use the Sequel II or IIe System and SMRT® Cell 8M to sequence to desired coverage depth for complexity
of genome
10- to 15-...
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Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?
I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to ...
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If a gene is expressed at a level of 1/1200 compared to the average gene, how is probability 50:50 that we have a read mapped to it?
I am reading a book about RNAseq analysis and it says
"To calculate the probability that a read will map to a specific gene, we can assume an average gene size of 4000 nt (100 M nt divided by 25,...
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Contamination on genome assembly
I had a question for the community.
I have a genome of a new species that has been sequenced via 150pb Illumina paired-end.
To verify the quality of the assembly I used the ...
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Calculating average coverage for .bam files (sequence data)
(Full discolosure that this is my first time working with sequence data, and with the bash scripting.)
I need to calculate the average coverage for any .bam file.
After some searching I wrote the ...
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Analyzing a blast result of NGS data
I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI.
I filtered those read data whose paired ends ...
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Bedtools wrongly indicates zero coverage
I have a BAM file produced using BWA-MEM and I need to calculate the coverage of each exon in this sequencing. I tried using this command:
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how to calculate coverage of each base of mapped reads?
I have a RNA aligned file without any header info.
I need to calculate the coverage of each mapped base for per chromosome. Is it possible to do it with perl ?
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How to choose reference to calculate coverage of WGS of organism that has high intra-species variation?
Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation ...
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bedtools coverage - Report the depth at each position in each A feature
I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected.
Instead it reported 0 coverage at every positions.
This is how I did ...
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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 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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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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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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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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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 ...
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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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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 ...
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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 <...
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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 ...
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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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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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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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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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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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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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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 ...
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