User: rahman.samir33

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Posts by rahman.samir33

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Comment: C: Bowtie2 build index
... Thank you for your reply! ...
written 7 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 7 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 7 months ago by rahman.samir330 • updated 5 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 7 months ago by rahman.samir330 • updated 7 months ago by genomax55k
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Comment: C: I can't install HiC-Pro
... MacOS. This is my laptop. ...
written 7 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 7 months ago by rahman.samir330 • updated 7 months ago by genomax55k
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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 7 months ago by rahman.samir330 • updated 7 months ago by genomax55k
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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 7 months ago by rahman.samir330 • updated 7 months ago by Biostar ♦♦ 20

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