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**Generate second coverage report with different options:**
Currently `bedtools genomecov` is used to create coverage reports for aligned bam files. This is great, but it would be helpful to also hav…
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bedtools closest -a a.bed -b b.bed -D b
I should find the same number of features in the first file (a.bed) as I haven't specified the maximum distance.
I wonder if there is a default distance…
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It would be really useful if there were a samtools utility that would allow one to shift read alignments by strand. _e.g._ shift all reads aligning to (+) strand up 5bps and all reads aligning to (-) …
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Hello
I try to run barrnap to identify rRNA from a eukaryotic genome , the commad as follow:
barrnap --kingdom euk --threads 20 --outseq rRNA.fasta < chr1.fasta
After running, we got followin…
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I'm having an issue with bedtools coverage throwing this error:
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Aborted
The command is as fol…
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Hi, I downloaded the respective FASTQ (SRR14765640-14765647) from Zhang et al. raw MeRIP-seq data (GSE151028) and generated the list of m6A sites using HISAT2 and MACS2 as described in the methods sec…
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```
using terminal on my mac OS X
followed installation protocol
typed in: curl http://bedtools.google... etc with version 2.17.0
Bedtools.tar.gz appeared on my desktop
I unzipped it
went into the fo…
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I am attempting to install via the instructions provided. I used git clone to download the repository. I ran configure.sh and everything succeeded (see below). I tried the make command and it came up …
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I have used bedtools version 2.28.0, where similar problem for bedtools jaccard (in version 2.26.0) is already solved, but not for fisher.
See example files below.
3CGvs1CGregion_chr1.bed (5786070…
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Hi,
I was trying to run LORALS, but it seemed that I fell into a dead loop.
First I created an independent environment named LORALS in conda, installed samtools as well as bedtools, and ran the code…