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Hitting an error in partition_bam_reads:
```
rule partition_bam_reads:
input: inputs/star_2_7_gencode40_sjdb/chrNameLength.txt, output/bams/dedup/genome/IP.genome.Aligned.sort.dedup.bam, annota…
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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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Hi, Thanks for creating bedtools @arq5x !
When I use:
`bedtools multiinter -header -i a.bed b.bed`
the resulting output looks like this:
```
chrom start end num list a.bed …
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can you please post the link to the BEDPE format specification that INTEGRATE-Neo requires? the fusions.bedpe and result.bedpe example files you provide are in formats different from this BEDPE format…
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Hi Oskar,
I got some problems about the depth calculation. I saw that BEDtools is used as the calculator for depth, and there is a perl script to calculate average depth. Previous calculation showe…
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For tools like bedtools, there are too many subcommands and not everyone is implemented for completion. Also most of them are not frequently used and maybe change by time.
Can we have a minimal fil…
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Does `genomecov` use non-primary alignments (secondary/supplementary) from the BAM in it's calculations? If so is there any in-built way to exclude them?
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Hi, I report a possible bug in `getfasta`.
It seems `-rna` option does not work for plus strand record when setting `-s` option.
Here is a test bed file (`test.bed`):
```
chr3 89235292 89235302 t…
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### Description of the bug
Failed to pull BEDTOOLS singularity image
### Command used and terminal output
```console
Sep.-20 18:49:13.796 [Task submitter] INFO nextflow.Session - [3b/0db9e9] Submi…
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### Is your feature request related to a problem? Please describe
- [x] bedtools/merge
- [x] bedtools/sort
- [x] cat/fastq
- [x] custom/dumpsoftwareversions
- [x] ensemblvep/vep
- [x] fastqc
- [x] ga…