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When I ran
bedtools unionbedg -i 1.bg 2.bg -name 1 2> union.txt
I got
bedtools: unionBedGraphs.cpp:99: CHRPOS UnionBedGraphs::ConsumeNextCoordinate(): Assertion `!queue.empty()' failed.
Aborted …
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Hi njaupan,
I am having an issue running the test Arabidopsis samples provide. It always crashes at the same point. I also tried running with my own samples and got the exact same problem at this p…
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Hello,
When running Get_DoGs_rpkm I get an error with bedtools (see below).
The solution would be "simple" in pinciple.
It should be to add the -g parameter to the bedtools command, and the user …
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If I run `bedtools annotate` with `-names`, then "names will be printed as a header line". That happens. However, the header in the `-i` file is gone. In other words, none of the columns are labeled …
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Hi,
I am running PAScall on my Cellranger3.0 output using ensembl v97 annotation (all annotation is ensemble / no "chr" pasted in front of the chromosome names).
PAScall runs until it starts usi…
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Hi,
I ran with the following command line for RDD:
java -jar $scriptPATH/JACUSA_v2.0.4.jar call-2 -p $nCPUs -F 1024 -a I,B,S,M,H:condition=1 -r $outPATH/$outFILE -f V -b $bedPATH/$bedFILE -R $genP…
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BEDtools version 2.26.0.
Example as follow:
mm10-NlaIII.bed:
chr1 0 3000185 HIC_chr1_1@chr1:0-3000185
chr1 3000185 3000316 HIC_chr1_2@chr1:3000185-3000316
chr1 3000316 3000850 HIC_chr1_3@chr1:300…
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Hi Aron,
As we have all our genomic fasta gziped for using with bwa, I was wondering if bedtools getfasta can work with gzipped data.
Pablo.
pamag updated
3 months ago
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Hello, I have the error when running `guidance = scglue.genomics.rna_anchored_guidance_graph(rna, atac)` when using the data provided in the tutorial. The error stated `"sortBed" does not appear to be…
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Note that the new version of `BEDTools` includes `htslib`. My first quick test build failed, so some changes will be required:
https://github.com/arq5x/bedtools2/releases/tag/v2.28.0