User: aropri

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aropri0
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Posts by aropri

<prev • 24 results • page 1 of 3 • next >
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(Closed) Cannot access interactive node
... This is not exactly a ChIP seq question, but when I type in source ~/.bashrc, it does not do anything. Normally I would run the command and it will change from "-bash" to "(base)-bash" and then I could run conda and its commands. Hoping someone can help me figure out why when I type in source~/.bash ...
chip-seq written 11 days ago by aropri0 • updated 11 days ago by JC11k
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Comment: C: Sicer peak calling
... I figured it out, no issues now. I converted bam file to bed and added chr as a prefix and it ran fine. Thank you so much! ...
written 28 days ago by aropri0
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Comment: C: Sicer peak calling
... Thank you so much. I did look at the documentation, I was running that command with my bam files but not getting any peaks. ...
written 5 weeks ago by aropri0
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Sicer peak calling
... Has anyone used Sicer to peak call using bam files and bed files. I would appreciate it if someone could help me get the command to do peak calling using treatment vs input bam files. Also, how does sicer use bed files to peak call, i thought peak calling was produced bed files. Would appreciate any ...
chip-seq written 5 weeks ago by aropri0 • updated 5 weeks ago by jared.andrews076.4k
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ROSE Algorithm for Ranking Super Enhancers
... I am trying to run ROSE after I have gotten my peak files and converted them to gff. I tried to use ROSE and it seemed ROSE_main.py failed to call ROSE_bamToGFF.py, with the following message: "sh: ROSE_bamToGFF.py: command not found" I called ROSE_main.py in the same folder that does contain ROSE_b ...
chip-seq written 5 weeks ago by aropri0
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Comment: C: Copy column to another column in the same file
... Thank you very much! ...
written 6 weeks ago by aropri0
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Comment: C: Copy column to another column in the same file
... Thank you for your help. It works, but how do I make the change permanent. ...
written 6 weeks ago by aropri0
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Copy column to another column in the same file
... I have a gff3 file with 9 columns, I want to copy the 9th column and its content to column 2 of the same file so column 2 and 9 will look identical. Was hoping if there is a way to do that. Appreciate all the help. ...
chip-seq written 6 weeks ago by aropri0 • updated 6 weeks ago by jared.andrews076.4k
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Comment: C: Using genome tools to convert bed files to gff3 files
... I figured it out. I had to create a python environment in ubuntu with python version 2.7 as genometools is only compatible with this version. Then I used conda to install this version: broad-viral / genometools-genometools 1.5.10. Then when i used the gt command it worked. Thanks for all your help. ...
written 7 weeks ago by aropri0
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Comment: C: Using genome tools to convert bed files to gff3 files
... Thank you for your answer. I tried genometools-genometools in ubuntu but I still get command not found. What could I be doing wrong? I appreciate all the help. ...
written 7 weeks ago by aropri0

Latest awards to aropri

Scholar 12 weeks ago, created an answer that has been accepted. For A: ChIP seq: Trying to use ChIPQC to measure quality of reads

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