User: jaeil.han

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jaeil.han10
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Location:
United States
Last seen:
1 year, 4 months ago
Joined:
3 years 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 16 months ago by jaeil.han10 • updated 16 months ago by Martin Čech ♦♦ 4.8k
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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 23 months ago by jaeil.han10 • updated 23 months ago by Jennifer Hillman Jackson25k
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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 2.8 years ago by jaeil.han10 • updated 2.8 years ago by Jennifer Hillman Jackson25k
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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 2.8 years ago by jaeil.han10 • updated 2.8 years ago by Jennifer Hillman Jackson25k
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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 2.8 years ago by jaeil.han10 • updated 2.8 years ago by Jennifer Hillman Jackson25k
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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 2.9 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 2.9 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 3.0 years ago by jaeil.han10 • updated 2.8 years ago by Martin Čech ♦♦ 4.8k
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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 3.0 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 3.0 years ago by jaeil.han10 • updated 2.8 years ago by Martin Čech ♦♦ 4.8k

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