User: rahman.samir33

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Posts by rahman.samir33

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Algorithms for HiC/HiChIP analysis
... Hi everyone, my name is Samir. I am a postdoctoral researcher at the Icahn School of Medicine of Mount Sinai in New York. We are in the process of deep sequencing HiC and H3K27ac HiChIP libraries. We are trying to figure out the best way to analyze the data for a pilot study. I've noticed that diffe ...
3d genome hichip hic written 9 weeks ago by rahman.samir330
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Comment: C: Bowtie2 build index
... Thank you for your reply! ...
written 10 months ago by rahman.samir330
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Bowtie2 build index
... Hi, I wanted to know how long it takes to build an index on bowtie2 using hg19. Bowtie2 creates 6 files with suffixes .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. .1.bt2, .2.bt2, .3.bt2, .4.bt2 have been created at least an hour ago. I am still waiting for the other two files. These ...
build index bowtie2 genome mapping written 10 months ago by rahman.samir330
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Create a BED restriction digest file in HiC-Pro
... Hi, I am trying to create a BED file in HiCPro containing all the restriction fragments created by DpnII. I have loaded the hg19.fasta file in the annotation folder. When I run the command HiC-Pro_2.10.0/bin/utils/digest_genome.py -r dpnii -o hg19_dpnii.bed hg19.fasta I get the following error mess ...
hic chromosome conformation capture hic pro written 10 months ago by rahman.samir330 • updated 8 months ago by Francis0
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Comment: C: I can't install HiC-Pro
... Hey, thank you so much! I dowloaded Anaconda and was able to install the missing Python libraries. This is the message I receive now: Starting HiC-Pro installation ... export /usr/local/Cellar/bowtie2/2.3.4 in PATH export /usr/local/Cellar/samtools/1.7 in PATH export /usr/local/Cell ...
written 10 months ago by rahman.samir330 • updated 10 months ago by genomax59k
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Comment: C: I can't install HiC-Pro
... MacOS. This is my laptop. ...
written 10 months ago by rahman.samir330
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Comment: A: I can't install HiC-Pro
... When I run "pip install bx-python", I get this message: Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/fq/hmbm61rx6bv9kpqhrjyycd9h0000gn/T/pip-build-aFTaS0/bx-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', ' ...
written 10 months ago by rahman.samir330 • updated 10 months ago by genomax59k
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Comment: A: I can't install HiC-Pro
... Hi, thanks for your replies. I realized I was in the wrong directory, and have actually advanced a bit. Here is the error message I receive now: Starting HiC-Pro installation ... export /usr/local/Cellar/bowtie2/2.3.4 in PATH export /usr/local/Cellar/samtools/1.7 in PATH ...
written 10 months ago by rahman.samir330 • updated 10 months ago by genomax59k
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I can't install HiC-Pro
... Hi everyone, my name is Samir. I am a postdoc at Mount Sinai. I am very new to genomics and computational biology. I am trying to install HiC Pro, but having difficulty doing so. I downloaded the HiC-Pro-2.10.0.tar.gz file and unzipped it. I ran the following code in the terminal as suggested and r ...
software error genome next-gen written 10 months ago by rahman.samir330 • updated 9 months ago by Biostar ♦♦ 20

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Bowtie2 build index

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