What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCoverageBed?
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4 months ago
kieft1bp • 0

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?

bedtools bam bed read mapping • 231 views
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4 months ago
ATpoint 48k

It extends coordinates to the 3‘ direction starting from the 5‘ position to the value you give it. You have to ask the developers why that is not available in the coverage function.

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Thanks for your simple answer. So, in my case from above, if I have a read that is 50 bp long it will be trimmed to 20 bp, and if I have a read that is 10bp it will be extended to 20bp in order to calculate final per-bp coverage?

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