Installing pybedtools in Windows 10 · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Installing pybedtools in Windows 10

I am trying to install pybedtools in Windows 10 Jupyter Notebook but it gives me following error:

pybed

Do we able to install pybedtools in Windows 10?

pybedtools

• 2,333 views • link

updated 3.3 years ago by i.sudbery

• written 3.3 years ago by anasjamshed

1 answer

No, it is not possible to use pybedtools in native windows, as it relies on the presence of bedtools, which is not available for windows. If you need to use pybedtools on a windows machine, you will need to do so via Windows Subsystem for Linux (WSL). You'll have to install jupyter and bedtools and pybedtools in there.

• 0 views • link

written 3.3 years ago by i.sudbery

Log in to answer this question.

More posts like this

Error while doing trimmomatic
written 2.1 years ago by dr.deepakkukkar •

Dear all, I am trying to do trimmomatic of the files: CRR503927_f1.fastq and CRR503927_r2.fastq in jupyter-lab. I am getting the error as shown in the …
TRIMMOMATIC ERROR ON WINDOWS/CYGWIN
written 3.1 years ago by Beyza •

Hi everyone, I am trying to install Trimmomatic and use it to RNA-seq in my Windows computer. But unfortunately, there is an error that I …
Problem while executing bedtools sort
written 3.3 years ago by anasjamshed

I want to execute bedtools sort -i S2.bed -g sizes.txt my genome file(sizes.txt) looking like: ![genome][1] [1]: /media/images/0eaf088c-89cb-403b-a245-2459daa7 But I am getting the following error: …
Failed to read and parse vcf file
written 4.5 years ago by anasjamshed

I am trying this code: ```py import vcf vcf_reader = vcf.Reader(open('C:/Users/USER/Desktop/isiah/VCFs_1/test_1.vcf', 'r')) for record in vcf_reader: print (record) ``` But its giving me import error …
Discordant results from the Scanpy tutorial "Preprocessing and clustering 3k PBMCs"
written 4.6 years ago by sbstevenlee •

Hello, I'm new to single-cell RNAseq analysis and have been trying to learn how to use the [scanpy](https://scanpy.readthedocs.io/en/stable/) program. To this end, I wanted to …
Unable to install pysam on windows 7
written 4.6 years ago by anasjamshed

I am trying to install pysam in windows by using pip install pysam but it is giving me error: ERROR: Command errored out with exit …
Installing SRAToolKit
written 5.4 years ago by hoffmavl1 •

Hi there, I am a complete newbie and trying to learn some of the basics. I need to install the SRAToolKit (https://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_LocalSRABlast_StepByStep.pdf) and cannot for …
Epi2me Lab on Windows 10
written 5.6 years ago by gatheringdusthere •

I'm just starting to explore Minion sequencing and am planning to install Epi2me Lab to go through the tutorials. Is it possible to run Nanopore's …
Error in WGCNA packages installation in R?
written 6.4 years ago by harshraje19 •

Dear all. I am trying to install the WGCNA, but whenever i install it, it gives me following error, Warning in install.packages : installation of …
Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook?
written 7.1 years ago by M.O.L.S •

I am analysing protein data using Python programming language and Jupyter notebook. In the Terminal I have put an alias in a hidden file on …