User: thackl

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thackl2.5k
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Posts by thackl

<prev • 221 results • page 1 of 23 • next >
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Comment: C: error for barplot in enrichGO(clusterProfiler)
... Made it bold, an put it in front of the instructions ;) ...
written 20 days ago by thackl2.5k
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Answer: A: error for barplot in enrichGO(clusterProfiler)
... I had the same problem. It is a general problem with the R graphics device. R's default backend for drawing graphics on X11 windows is "Xlib", and that uses the x11-font that doesn't work. From what I understand those x11 fonts are discouraged on current linux distros (not sure about other OS's). ...
written 21 days ago by thackl2.5k
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Comment: C: How to run velvet multithreaded?
... No, sorry I don't. But I think that it is not unlikely. ...
written 10 months ago by thackl2.5k
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Answer: A: Bimodal GC content
... I don't think that you can necessarily extend the observations made above to directly to RNASeq experiments. Also, I don't really know if a bimodal GC distribution is something to be concerned about in the first place when looking at RNAseq. You might need to talk to people more involved with RNASeq ...
written 11 months ago by thackl2.5k
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Comment: C: Dowload all complete genomes grom GenBank .gbk full format
... To elaborate a bot on 5heikki's suggestion: The following commands for example should download all complete genome assemblies for E.coli (taxid: 562) wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -v taxid=562 -v status="Complete Genome" -F $'\t' '$7==taxid ...
written 22 months ago by thackl2.5k
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Comment: C: ALLPATHS-LG slow ... multi threads possible ?
... What was your solution?? Up to 5TB for 3Gbp plant genome. ...
written 23 months ago by thackl2.5k
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Comment: C: Is there a term for a genome assembly that is not closed?
... And technically, even a draft assembly can be closed :) ...
written 23 months ago by thackl2.5k
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Answer: A: Is there a term for a genome assembly that is not closed?
... What [5heikki][1] said: draft genome assembly [1]: https://www.biostars.org/u/9490/ ...
written 23 months ago by thackl2.5k
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Comment: C: ALLPATHS-LG slow ... multi threads possible ?
... I did experience some weird problems with ALLPATHS-LG in the past on some machines that could be similar to what you are experiencing - I never really figured out the real reason or how to fix it, though. In my case, once a certain amount of RAM was loaded with data (ALLPATHS reads entire libraries ...
written 24 months ago by thackl2.5k
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Comment: C: ALLPATHS-LG slow ... multi threads possible ?
... 1) Yes, that's what I did. I split up my original file in serveral groups/libs.csv and imported those. 2) As far as I understand, if you just provide a single number, it will set the number of forked processes (libraries processed in parallel) on the current node, i.e. it more or less should be equ ...
written 24 months ago by thackl2.5k

Latest awards to thackl

Appreciated 7 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Appreciated 13 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Popular Question 15 months ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 20 months ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 2.5 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 2.7 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 3.0 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 3.0 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Scholar 3.0 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance

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