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When students attempted to run the genomecov command via bedtools, uniformly the process died at some point.
However, the same command executes just find from the main course project. Perhaps some…
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Thanks for the great tool!
I'm a bit unclear why there is a difference between the number of overlapping peaks found by bedtools overlap and findOverlaps (which find the exact same number of overla…
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Needed for `-name+` option.
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Error: to calculate BAF values, you need to provide mateFile in SAMtools pileup format
Or you can set 'makePileup' parameter true by providing a path to a VCF file with SNP position
`###For more …
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Hi !
Thanks for the amazing pipeline! I remember reading before, but couldn't find the details now, so here I am. What is the number in the TAR read before _0 or after the strand? Is it the number of…
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In the Bedtools build, the file /tmp/launch_bedtools.sh isn't present.
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Hi,
I developed an app that a) uses the bedr R package (that requires 'bedtools' as third party tool) and b) is running a python script with bedtools requirement using a system command in the shiny …
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I am trying to use findZX on reads that have already been trimmed, but I keep getting an error that only happens when I skip the trimming part of the pipeline.
Is there a way around this? Or should…
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BP3 section here: https://github.com/arq5x/bedtools-protocols/blob/master/bedtools.md
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I am trying to train ChromBPNet on Arabidopsis ATAC-seq data, but run into the error `"Input file shifts inconsistent"` as in #153, #174 and #176. Having read through these other issues, I was able to…