User: thackl

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thackl2.4k
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Posts by thackl

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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 24 days ago by thackl2.4k
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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 weeks ago by thackl2.4k
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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 12 months ago by thackl2.4k
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Comment: C: ALLPATHS-LG slow ... multi threads possible ?
... What was your solution?? Up to 5TB for 3Gbp plant genome. ...
written 14 months ago by thackl2.4k
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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 14 months ago by thackl2.4k
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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 14 months ago by thackl2.4k
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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 14 months ago by thackl2.4k
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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 14 months ago by thackl2.4k
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Answer: A: ALLPATHS-LG slow ... multi threads possible ?
... It is a bit tricky, but you can speed up data import by setting up a cache first with `CacheLibs.pl/CacheGroups.pl`. See "ALLPATHS Cache for power users", page 19 in the manual for details. With those scripts you can add different libraries individually and in parallel, and CacheGroups.pl also allo ...
written 14 months ago by thackl2.4k
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Answer: A: Confusion about the term genome coverage
... The sum is correct: 35x Genome coverage in the most simple way means the mean per-base coverage of the genome given a set of reads (can be multiple libraries). I.e. if you have a genome of 1000bp in length and 10 reads of 100 bp, than you coverage is `(10*100bp)/1000bp = 1`. If you have 100 reads, ...
written 16 months ago by thackl2.4k

Latest awards to thackl

Appreciated 3 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Popular Question 6 months ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 11 months ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 19 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 21 months ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 23 months ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 2.2 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Scholar 2.2 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Scholar 2.2 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 2.3 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance

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