Measure Sequencing Depth in aligned BAM file
I have some aligned BAM files and I want to calculate the sequencing depth, but numerous google searches have not produced any results. I could generate a tool by myself, but I want to use something which has been used by others so that there is less room for error.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Annotate GFA with coverage depth
written by elcortegano
-
statistical power calculation for array data
written by dec986
-
Genewiz gave me bam files instead of fasta files- can I convert bam to fasta to have a genome assem…
written by kristina.mahan
-
sorted bam file
written by evelyn
-
searching tool for calculating switch/phase error rate
written by WouterDeCoster
-
What tools can I use to calculate sequencing depth and sequencing coverage for ddRADseq data
written by jingjin2203 •
-
Searching Gene Ontology for Known Organs
written by dec986
-
defintion of extremely low coverage
written by statfa
-
Tools to view fastq file
written by Roden Luo •
-
Calculating Depth For Each Amplicon From A Mapped Bam
written by Robert Sicko
What was wrong with, say, samtools depth? Or bedtools coverage? if you can explain why those were not suitable people might be better able to direct you to what is suitable.
In addition, are you interested in read-depth over a particular genomic position?; are you interested in the target depth of coverage to which your samples were sequenced?; the number of bases that reached a particular depth of coverage (e.g. 10x, 20x, 30x, etc?).
You must be more specific.