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This is more of a support request/usage question. Is there a better venue for those?
I want to select the strongest peak among replicate ChIP experiments. Inspired by these [docs](https://bedops.r…
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I have a [bed-like file](https://www.meuleman.org/research/dhsindex/) with identical start/stop coordinates. When I try to `sort-bed` I get
```
Genomic end coordinate is less than (or equal to) star…
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Hi,
Thanks a lot for the great tool and nice vignettes, which are super helpful!
I have a question regarding your RNA+ATAC tutorial (http://htmlpreview.github.io/?https://github.com/welch-lab/li…
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I am using bedmap version: 2.4.38 .
I run the following:
bedmap --echo --echo-map-id-uniq --skip-unmapped gencode.v29.gene.bed $f > $out_file
where gencode.v29.gene.bed is gecode v 29 gtf f…
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Hi Florian,
I am trying to run your deconvolution script on my bismark methylation extraction file (.bedgraph or CX-report). Can you please tell me how have you created the sample methylation bed fi…
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I was running bedmap with this command:
```
/hpc/tools/BEDOPS/bin/bedmap \
--ec --skip-unmapped --delim '\t' --prec 0 --fraction-map 0.5 --echo --sum \
/hpc/tools/BEDOPS/hg38_chromSizes2_sort_500b…
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Hi,
I have encountered several problems when trying to make a gene activity matrix from scATAC-seq data. When I tried to follow the instructions in your tutorial (https://macoskolab.github.io/liger…
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Hi,
it seems this used to work with gencode_v21 but not with v28, v29, v35 which I tried so far.
ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_21/gencode.v21.annotation.gtf.gz
ftp.e…
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Hi,
Recently I tried to use bedmap to count the overlap of two bed.files.
One ref-bed file is like:
######
chr11 3000000 4000000
chr11 4000000 5000000
chr11 5000000 6000000
chr11 6000000 700000…
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While trying to convert vcf to bed I came across the following error:
```
vcf2bed < trimmed.FAM1_MU006.nanovar.pass.vcf
Start coordinate is too large. Max decimal digits allowed is 12 in BEDOPS.…