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I should install all softwares mentioned in the last rows of the file 'config.yaml', including:
atacqc: "/mnt/public3/cat/data/ATAC/atacqc"
trimmomatic: "~/miniconda3/bin/trimmomatic"
bwa: "~…
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```
I attempted to do an anonymous svn checkout using this command
svn checkout http://bedtools.googlecode.com/svn/trunk/ bedtools-read-only
But my bedtools-read-only directory does not contain any …
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help message shows that -5 mean "calculate coverage of 5' positions instead of entire interval", but I don't know what's 5' position exactly means?
ZHANG Yan
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bedtools coverage is quite slow for reasonably size files -- at least with -abam.
It seems a common thing to want to do something like:
```
bedtools coverage -abam my.bam -counts \
-b
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Hi!
I have tried for a few days now to understand why I sometimes get different subsequences than using 'bedtools getfasta' from hg19 reference. I was wondering if you could elaborate the indexing …
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Hi,
I have question about values obtain from bedtools and intervene of Jaccard similarity.
**Command bedtools jaccard in bash script:**
```
bedtools jaccard -a "$file1" -b "$file2" -f 1.0 -r -…
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Hello! Thank you for providing such a useful software.
My original hic data are all paired reads of equal length of 150bp. I hope that the simulated data are also regular 150bp paired reads.
Bu…
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I've had a lot of trouble installing conda environments from LCR-modules recently. Many of the environment yaml files seem to contain packages that are no longer available or now conflict with other s…
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Counts the reads mapped to constructs of interest between the two methods can differ up to 500 reads. Partially because intersect currently does not account for multimapped reads but mostly because th…
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Hi! In your README.me you suggest using a series of four steps to create a bedgraph file for input to SEACR.
```
bedtools bamtobed -bedpe -i $sample.bam > $sample.bed
awk '$1==$4 && $6-$2 < 1000 …