User: Mesohexaploid

Reputation:
10
Status:
New User
Location:
Last seen:
2 months, 3 weeks ago
Joined:
8 months, 4 weeks ago
Email:
h*********@hotmail.de

Just a plant scientist who fell down the bioinformatics hole. Currently on the hunt for a PhD position. PhD student.

Posts by Mesohexaploid

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Problem with dependencies: Conda/freebayes
... Hello Devon, Thank you for your response. It appears to be that the dependency issue was somehow resolved after the n-th attempt at re-installation. Regards ...
written 7 months ago by Mesohexaploid 10
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Comment: C: Problem with dependencies: Conda/freebayes
... Yes, the tools, parallel, and our entire Galaxy instance. The issues remained... ...
written 7 months ago by Mesohexaploid 10
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Problem with dependencies: Conda/freebayes
... Dear Galaxy Team, We encountered a problem while installing freebayes and its dependencies via Tool Shed. Galaxy correctly installed freebayes (1.1.0.46), samtools (0.1.19) and gawk (4.1.3) (all have the Current Installation Status "Installed through Conda"), but then failed on the last dependenc ...
freebayes tool shed conda written 7 months ago by Mesohexaploid 10
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Answer: A: Are there maximum Penalty Scores in BWA-MEM?
... Hello again, I'm just going to answer my own question here in case there is anyone else who would like to know the answer to this (doubtful). [I asked this question in the non-Galaxy Biostars][1], and basically, there are no maximum penalty scores and the scores in the square brackets represent th ...
written 8 months ago by Mesohexaploid 10
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Comment: C: Can contamination cause alignment errors and how can I trim contaminants away?
... Thanks again Jennifer, So I interlaced my reads after grooming, then trimmed them for quality, then de-interlaced them and separately loaded the forward and reverse reads into HISAT2. I almost thought the output was empty again but then I scrolled really far down and, lo and behold, alignments had ...
written 8 months ago by Mesohexaploid 10
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Comment: C: Can contamination cause alignment errors and how can I trim contaminants away?
... Hello Jennifer, Thanks for your swift response! I'll stick with HISAT2 for now. Unfortunately, the BAM file produced by HISAT2 only contained a list of QNAME but nothing else. I'm still trying to determine what is wrong with either the reference sequence or my reads to have caused this. The refer ...
written 8 months ago by Mesohexaploid 10
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Can contamination cause alignment errors and how can I trim contaminants away?
... Hello Galaxy Team, Sorry if this question is all over the place. I have been trying to align some RNA seq reads (each around 6 million reads in size) against a diploid plant genome (32,928 sequences). However, I cannot seem to get it aligned. Both RNA STAR and TopHat2 give me different error mes ...
rna star trimming alignment rna-seq written 8 months ago by Mesohexaploid 10 • updated 8 months ago by Jennifer Hillman Jackson25k
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Comment: C: Problems with connection to FTP server (SSL/TLS required)
... Hello Utkarsh, Thanks for the response. I've tried using WinSCP and SpeedCommander as well, but they also returned error messages. I'm not sure if the client is the issue. Our Firewall doesn't seem to be causing any problems either. What encryption settings do you have? Regards ...
written 8 months ago by Mesohexaploid 10
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Problems with connection to FTP server (SSL/TLS required)
... Hello again Galaxy Team, I'm trying to upload two fq.gz files, each around 4GB in size. When trying to upload the files directly, I get the error message: Failed: File exceeds 2GB. Please use a FTP client. This is strange because I remember uploading an 8GB file using this method around two weeks ...
error message ftp upload written 8 months ago by Mesohexaploid 10 • updated 8 months ago by utkarsh.kapoor50
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Answer: A: Listing genome reference
... Hello, I am also interested in the addition of a wheat reference genome. From what I understand, genome additions can be requested here: https://github.com/galaxyproject/galaxy/issues/1470 However, if you look at the thread, Triticum aestivum is already listed as being under review (since Apr ...
written 8 months ago by Mesohexaploid 10

Latest awards to Mesohexaploid

Popular Question 4 months ago, created a question with more than 1,000 views. For Problems with connection to FTP server (SSL/TLS required)
Supporter 4 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Are there maximum Penalty Scores in BWA-MEM?
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.

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