Hello, I am trying to merge and average three BedGraph files using the following code on terminal: bedtools unionbedg -i file1.bedgraph file2.bedgraph file3.bedgraph | awk 'OFS="/t" {sum=0; for (col=4; col<=NF; col++) sum += $col; print $1, $2, $3, sum/(NF-4+1); }' > averaged_file.bedgraph
I get the following error message:
bedtools: src/unionBedGraphs/unionBedGraphs.cpp:99: CHRPOS UnionBedGraphs::ConsumeNextCoordinate(): Assertion `!queue.empty()' failed.
Aborted (core dumped)
I have tried to sort the files using
sort -c -k1,1 -k2,2n <file.bedgraph>
But I get the following error message:
sort: file1.bedgraph:2: disorder: . -1 -1 -1
The head of my BedGraph files (image below) looks like this, so it appears to be in tab-delimited format:
Any advice on why this is failing and possible solutions will be really appreciated! Thanks.
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you're not sorting anything here.
-cis just for checking the file is already sorted.-1is not a valid bed coordinate.Thank you, I thought it looked weird. These were in the bed file from which I generated the BedGraph -- do you have an idea of how they've arisen?
Also, thank you for pointing out the "-c" flag error above.
Try deeptools it has many tools for
bedGraphandbigWigfiles.Hi, thanks for the suggestion! Based on deeptools documentation, it looks like multiBigwigSummary might be the one for me:
but it gives a compressed numpy array output (.npz). Do you know whether it's possible to convert .npz to other formats, such as .bg, .bed, or .bw? I'm struggling to even find exactly what data ends up in this .npz file, so I can't figure out a way to convert it to other file types. Thanks again!
It seems that my comment was misleading. There is
--outRawCountsoption but it's output is tab-delimited, I have not tested it. I don't know if it's possible to convertnpzto other formats. I used it to plotting. There is bigwigCompare command which have--operationoption and it can bemeanbut it works only for two files.Consult this post , it seems that
wiggletoolsaverageswigfiles. So you can convertbedGraphtobigWigand after averaging makebedGraph. There are tools indeeptoolsand kentutils which can be helpful.Thanks very much, I also found this post yesterday and it seems it might be just the thing. Thanks again for your help!