It works, thank you!
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kirillkirilenko •
Make a BedGraph file
I have a simple BED file displays repetitive elements localization (this file was obtained using RepeatMasker).
Here are the first few rows::
2L 840 882 Simple_repeat
2L 2763 2796 Simple_repeat
2L 3409 3498 DNA/Helitron
2L 5405 5432 Simple_repeat
2L 8844 9132 LINE/unknown
Now, I would like to create a BedGraph file that displays the coverage of repetitive elements per selected bin. Let's assume the bin size is 3000. The desired file should look like this::
2L 1 3001 0.025
2L 3001 6001 0.0387
where 0.025 is calculated as ((882-840)+(2796-2763))/3000.
I can write a Python code to accomplish this, but I believe there might be ready-made tools available for this task. Could you assist me? Thank you in advance.
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2 answers
Bedtools window piped into genomecov?
https://bedtools.readthedocs.io/en/latest/content/tools/window.html
https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
Or perhaps genomecov paired with awk? I'm thinking something like:
genomeCoverageBed -d -bg | awk 'begin{sum=0;} {sum=sum+1;if(NR%3000==0){print sum;sum=0;}}'
Disclaimer: I have not tested either of these strategies
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows. Maybe:
bedtools makewindows -w 3000 -g chrom_sizes > windows.bed
bedtools coverage -a windows.bed -b repeats.bed > coverage.bed
cut -f1-3,7 coverage.bed > coverage.bg
the cut command is because bedtools coverage outputs 4 extra columns, with the forth being "The fraction of bases in A that had non-zero coverage." If you use this command or otherwise have a minimal bed, columns 1-3 & 7 will produce your bedgraph. Otherwise, you will need to adjust column number of the fraction.
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