User: jaeil.han

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jaeil.han10
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New User
Location:
United States
Last seen:
8 months ago
Joined:
2 years, 4 months ago
Email:
j********@uth.tmc.edu

Posts by jaeil.han

<prev • 12 results • page 1 of 2 • next >
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Tophat is not provided anymore?
... I don't see Tophat in galaxy. I wonder if it is no longer available or it is just temporary. Can anyone help me with this issue please? Thanks in advance ...
tophat written 8 months ago by jaeil.han10 • updated 8 months ago by Martin Čech ♦♦ 4.3k
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how to extracts mRNA sequences with different Poly(A)tail lengths from RNA seq data
... I am trying to compare poly(A) tail length of mRNAs in cells with different condition both at global and individual mRNA levels. However, I don't know where to start. I think I could somehow extract mRNA sequences with polyA tail from BAM file after mapping? Can anyone give me an insight? Thanks, ...
polya mrna rna-seq written 15 months ago by jaeil.han10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Tophat somehow makes Cufflinks lose ribosomal RNA
... Hello, I am mapping yeast RNA seq data (ribozero) using Tophat followed by Cufflinks, Cuffcompare, and Cuffdiff to see differential gene expression. After Cuffdiff, I found that ribosomal RNA reads are all missing, while they are not missing when I used Bowtie2 for mapping. Only difference was tha ...
cufflinks tophat ribosomal rna written 2.1 years ago by jaeil.han10 • updated 2.1 years ago by Jennifer Hillman Jackson23k
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Trying to find antisense transcripts. Can Cufflinks in Galaxy specify library type?
... Hello, I am trying to find antisense transcripts, and mapping stranded reads to reference genome using Tophat (library type specified to fr). I wonder if I have to specify the library type in Cufflinks as well because I can't find the library type option in Cufflinks of Galaxy. I am afraid if I hav ...
cufflinks written 2.1 years ago by jaeil.han10 • updated 2.1 years ago by Jennifer Hillman Jackson23k
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Cufflinks assembles very small number of transcripts from RNA-seq data
... I mapped RNA-seq data to reference genome and tried to assemble transcripts using cufflinks.It is ribosomal RNA depleted samples from yeast RNA. In the mapped BAM files, I can clearly see many reads in many noncoding RNA genes using genome browser, but they are all missing in the results of cufflin ...
cufflinks rna-seq written 2.2 years ago by jaeil.han10 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Answer: A: Trying to run a Tophat on a local galaxy server but it gives me an empty bam fil
... I actually found the Bowtie2 but it says No Items when I tried to install. ...
written 2.3 years ago by jaeil.han10
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Trying to run a Tophat on a local galaxy server but it gives me an empty bam file and following message: galaxy_27.sh: line 29: bowtie2-build: command not found
... I am trying to run a Tophat on a local galaxy server but it shows a following message. I guess I need Bowtie2 installed. I already installed bowtie but I cannot find bowtie2 in tool_shed   Log: tool progress Log: tool progress /Users/jaeilhan/Downloads/galaxy-dev/database/job_working_directory/00 ...
galaxy written 2.3 years ago by jaeil.han10
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Comment: C: Local galaxy is not run on new Mac OSX (El capitan)
... I wonder if I did something wrong. Here is the part of the five.py file including the change I made. if sys.version_info < (3, 3):     import platform     SYSTEM = platform.system()     if SYSTEM == 'Darwin':         import ctypes         from ctypes.util import find_library         libSystem ...
written 2.3 years ago by jaeil.han10 • updated 2.1 years ago by Martin Čech ♦♦ 4.3k
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Comment: C: Local galaxy is not run on new Mac OSX (El capitan)
... I see! However, I made the change you suggested as well but got the same error.   ...
written 2.3 years ago by jaeil.han10
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Answer: A: Local galaxy is not run on new Mac OSX (El capitan)
... I reinstalled the galaxy and got something different. (It seemed to work at the beginning) https://gist.github.com/anonymous/6bb0846a894c1fe60e43 ...
written 2.3 years ago by jaeil.han10 • updated 2.1 years ago by Martin Čech ♦♦ 4.3k

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