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.

Filter by
Sorted by
Tagged with
1
vote
1answer
20 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 ...
1
vote
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...
4
votes
3answers
64 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 ...
1
vote
0answers
46 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 ...
4
votes
2answers
136 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 ...
1
vote
0answers
96 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 <...
5
votes
4answers
547 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 ...
1
vote
1answer
49 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 (...
6
votes
1answer
70 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 ...
1
vote
1answer
47 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 ...
3
votes
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}{...
7
votes
1answer
395 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: $$C = L*N / G$$...
7
votes
1answer
126 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 ...
3
votes
1answer
735 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 ...