bedGraph compress tools
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6.0 years ago

I'm trying to compress my bedGraph file because of the USCS file size limit, and was trying to use bedtools merge to collapse it on the score column but it merges too much (if the features are less than 1bp apart, it merges them together, so in a peak region it merges the whole peak). Is there a tool that collapses every n-bp in a bed file and calculates the mean of the score (column 4)? From my bedGraph:

chr1    11585   11587   0.00465
chr1    11587   11592   0.0062
chr1    11592   11615   0.00775
chr1    11615   11631   0.0093
chr1    11631   11642   0.01085
chr1    11642   11656   0.0124
chr1    11656   11667   0.01395

If I want to collapse every 30 bps, my output would be:

chr1    11585   11615   0.00775
chr1    11615   11645   0.010075
chr1    11645   11667   0.013175

I know that I can convert bedGraph to bigWig but I'd like to keep bedGraph format and just decrease its resolution if it's possible.

bedtools bedGraph • 2.8k views
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I think you have two options:

  1. Use e.g. deeptools bamCoverage with the -bs parameter that allows to set a bin size that the reads are aggregated over for your bedGraph, or
  2. Simply compress the bedGraph you have with gzip to reduce its size
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I tried bamCoverage. It worked really well, only had to play with the bin sizes a few times. Thank you!

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Why would you like to keep it in bedGraph format? That's a really annoying format to deal with if all you want is to visualize data.

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I don't really have a free host website to share the files on, so it's much easier to upload it to GB...

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Do you rely on UCSC? THere are alternatives like the IGV, that can read bigwigs from disk.

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Right, but I need to upload the data and share it with my boss, UCSC is the easiest way to do that. If it was for just myself, wouldn't been a problem...

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Do you need bins of equal size for some subsequent analysis, or only for compressing your file?

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No, I need just bins for the compression

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