User: Shellfishgene

gravatar for Shellfishgene
Reputation:
30
Status:
New User
Location:
Germany
Last seen:
3 months ago
Joined:
4 years, 10 months ago
Email:
t*********@gmail.com

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Posts by Shellfishgene

<prev • 11 results • page 1 of 2 • next >
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Interpreting dispersion plots in RNAseq analysis
... I have a RNAseq experiment I'm analyzing, using the Tuxedo pipeline. One of the suggested plots in cummRbund is a dispersion plot that plots dispersion against mean counts. I understand what the plot shows, however I'm not sure about the interpretation. I have an example from cummRbund below, 3 trea ...
disperson rna-seq written 24 months ago by Shellfishgene30
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Comment: C: Minia exits with error in "Debloom: cascading" stage
... Ok, that makes sense, so when I was running fewer Minia jobs the chance that there was that file conflict was lower, that's why it worked. Thanks! ...
written 2.6 years ago by Shellfishgene30
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Comment: C: Minia exits with error in "Debloom: cascading" stage
... Hi Rayan, actually I noticed of 10 jobs only about half had the problem. I started them again with the exact same settings, and most of them finished. The one's that did not I just restarted a third time and now all worked. The problem seems to be intermittent, maybe it's caused by our cluster rath ...
written 2.6 years ago by Shellfishgene30
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Minia exits with error in "Debloom: cascading" stage
... Hi! I'm trying to run minia for an assembly, but I get an error in the "Debloom: cascading" step: [DSK: Collecting stats on read sample   ]  100  %   elapsed:   0 min 21 sec    estimated remaining:   0 min 0  sec   cpu:  147.4 %   mem: [ 51,  51,  51] MB [DSK: Pass 1/1, Step 2: counting kmers  ] ...
minia error written 2.6 years ago by Shellfishgene30
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Comment: C: Problem Compiling Bam-Readcount
... Thanks, version 0.4.6 compiled as described in the readme. The Boost library location was always set for cmake with env variables, so it seems the current version does something different. ...
written 4.0 years ago by Shellfishgene30
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Comment: C: Problem Compiling Bam-Readcount
... Thanks, I did mention cmake in the question. The problem seems to have been the version of bam-readcount, see below. Worked with local install of cmake and Boost even! ...
written 4.0 years ago by Shellfishgene30
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Comment: C: Problem Compiling Bam-Readcount
... The command line is "make" ;). I think -L does not apply here as it's cmake? I gave cmake the location of Boost with environment variables, as per the instructions. If I don't do that it doesn't even start to compile things, so that's somewhat working at least. ...
written 4.0 years ago by Shellfishgene30
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Problem Compiling Bam-Readcount
... Hi! I'm trying to compile bam-readcount on SUSE Linux (without root rights, this is our cluster). I seem to have a problem with Boost, I get a bunch of errors similar to this: bamreadcount.cpp:(.text+0x32f4): undefined reference to `boost::program_options::options_description::m_default_line_lengt ...
written 4.0 years ago by Shellfishgene30 • updated 4.0 years ago by ernfrid380
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Comment: C: Error Compiling Somaticsniper
... Indeed that was the error, I had used a wrong path in SAMTOOLS_ROOT. ...
written 4.1 years ago by Shellfishgene30
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Weird Samtools Mpileup Error In Mplp_Func.
... Hi! What is samtools mpileup trying to tell me with this error (or warning): [mplp_func] Skipping because 298 is outside of 0 [ref:103424] There are many like it. I double checked that I have the same reference fasta in the mpileup and the actual bwa mem mapping commands, and I do. Cheers ...
samtools mpileup error written 4.1 years ago by Shellfishgene30 • updated 3.5 years ago by ketilm41710

Latest awards to Shellfishgene

Popular Question 4 months ago, created a question with more than 1,000 views. For Interpreting dispersion plots in RNAseq analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For Problem Compiling Bam-Readcount
Popular Question 23 months ago, created a question with more than 1,000 views. For Weird Samtools Mpileup Error In Mplp_Func.
Popular Question 23 months ago, created a question with more than 1,000 views. For Error Compiling Somaticsniper

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