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2 hours ago by

United States

I am trying to extract per-base read mapping coverage from a BAM file based on several regions of interest in a BED file. For example, I want to get the coverage at each base pair for the following 1kb regions:

chr start   end name    score   strand
chrI    182604  183604  region1 0   -
chrII   197700  198700  region2 0   -
chrII   326866  327866  region3 0   -
chrII   643079  644079  region4 0   +
chrIII  82534   83534   region5 0   +

My current approach is to use:

coverageBed -a BED -b BAM -g GENOME_FILE -d -s > coverage.txt

I know what the coverage is "supposed" to look like (I'm trying to replicate a graph from a paper), and this command gives me something close but not exact. However, I can recreate it perfectly using the (much slower) process of calculating coverage for every base pair of the ENTIRE genome, then extracting specific regions using awk/grep scripting, as long as I use the "-fs" (fragment size) parameter set to 20 in genomecoverageBED:

genomecoverageBed -ibam BAM -d -strand + -fs 20 > coverage_pos.txt
genomecoverageBed -ibam BAM -d -strand - -fs 20 > coverage_neg.txt
a bunch of unix data wrangling to filter to only my regions of interest

My question is not about helping me solve this problem, I simply want to know: what exactly is the "-fs" parameter doing in genomecoverageBed and why isn't it an option with coverageBed?

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