User: yena.oh

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yena.oh70
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70
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Canada
Last seen:
3 weeks, 5 days ago
Joined:
1 year, 7 months ago
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y******@mail.utoronto.ca

Posts by yena.oh

<prev • 31 results • page 1 of 4 • next >
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Cannot find files - Bowtie2 or Tophat
... Hello, I have loaded 16 fastq files - 15 of which were moved from another history, and 1 file which was recently loaded to galaxy through FTP. I am only able to see the 1 file loaded through ftp when I attempt to run bowtie/tophat. On HISAT2 or fastQC, however, I see all 16 files. Any suggestions ...
fastqsanger input datatype tool fastq written 6 weeks ago by yena.oh70 • updated 6 weeks ago by Jennifer Hillman Jackson23k
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FastQC error-The server could not complete the request
... Hi there, I am trying to run the FastQC, but am getting the following error: The server could not complete the request. Please contact the Galaxy Team if this error persists. { "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65", "tool_version": "0.65", "inputs": { ...
fastqc error usegalaxy.org job fastq written 13 months ago by yena.oh70 • updated 13 months ago by Jennifer Hillman Jackson23k
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Answer: A: Why I can't use some of the tools
... Hi, For FASTQ joiner to work, your fastq files need to have its quality format changed to a fastqsanger format. This is done using the FASTQ Groomer tool. Run Groomer on your fastq files, then try doing running FASTQ joiner. Hope this helps! Yena ...
written 19 months ago by yena.oh70
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Comment: C: cuffdiff error and time
... Sorry about that. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/ ...
written 19 months ago by yena.oh70
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Answer: A: Errors in post alignment files
... By videos, are you referring to visualizing the reads alignment? Once the metadata was set with the warning message gone, visualizing also started worked for me. See if it works! Yena ...
written 19 months ago by yena.oh70
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Answer: A: Errors in post alignment files
... Hi Joe, I have also been having similar problems lately. For me, I resolved the issue by "editing attributes" by clicking on the eye icon on the right, and clicking on "auto-detect." Most of the times, the problem was solved. On files where auto-detect didn't work, simply re-running the analysis an ...
written 19 months ago by yena.oh70
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Answer: A: zero fpkm value in cufflink
... Hi, From your other post, it seems like there is an error with your reads alignment (tophat) step, as you had 0% of the input reads that were aligned to the reference genome, which would lead to fpkms of zero. Check your other post for suggestions: https://biostar.usegalaxy.org/p/17456/ Good luc ...
written 19 months ago by yena.oh70
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Answer: A: cuffdiff error and time
... This means that tophat did not work. Only 1226 reads out of 19118751 reads were aligned to the reference genome, hence 0.0% of input. Double check if you had provided the correct reference genome. Did you run a quality check on your reads (i.e. fastQC)? This will allow you to see if the reads are ...
written 19 months ago by yena.oh70
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Comment: C: is there a size limit for uploading sequence files?
... Hi Xiaofei, I use filezilla to upload my data that is 100GB and it works fine with the following information: Host: main.g2.bx.psu.edu Username: (your username) Password: (your password) Port: 21 Would this work? Yena ...
written 19 months ago by yena.oh70
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mm10 built-in reference genome unavailable
... Hi, I'm trying to run cuffdiff with bias correction: perform bias correction 'yes' -> Reference sequence data 'locally cached' -> Using Reference Genome I have run cuffdiff previously with this option selected and I was able to select "Mouse(Mus Musculus) mm10." However, now mm10 first sh ...
cuffdiff rna-seq written 19 months ago by yena.oh70 • updated 19 months ago by Jennifer Hillman Jackson23k

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Student 19 months ago, asked a question with at least 3 up-votes. For mm10 built-in reference genome unavailable

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