User: Mesohexaploid

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2 weeks, 5 days ago
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h*********@hotmail.de

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

Posts by Mesohexaploid

<prev • 7 results • page 1 of 1 • next >
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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 3 days 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 4 days 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 5 days ago by Mesohexaploid 10 • updated 5 days ago by Jennifer Hillman Jackson23k
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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 13 days 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 13 days ago by Mesohexaploid 10 • updated 13 days 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 13 days ago by Mesohexaploid 10
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Are there maximum Penalty Scores in BWA-MEM?
... Apologies if this is a simplistic question, I am new to Galaxy. I am working on a variant calling workflow for paired DNAseq reads, with BWA-MEM as my aligner. Since I have custom parameters, I would like to manually enter them into BWA-MEM through the "Select full list of options" category. I wa ...
bwa bwa-mem alignment written 19 days ago by Mesohexaploid 10

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