User: thackl

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thackl2.4k
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Posts by thackl

<prev • 218 results • page 1 of 22 • next >
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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 21 days 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 10 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 12 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 12 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 12 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 12 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 12 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 12 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 15 months ago by thackl2.4k
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Answer: A: Extracting reads mapped to any of multiple references
... If you store your bwa output in bam, rather than sam, you an use `samtools view -b -f 0x2 alignment.bam REGION`, with REGION being a single or multiple reference sequence IDs ``` samtools view -b -f 0x2 alignment.bam ref1 ref2 refx | samtools fastq ... ``` ...
written 15 months ago by thackl2.4k

Latest awards to thackl

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Popular Question 4 months ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 9 months ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 17 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 19 months ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 22 months ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Appreciated 22 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Teacher 24 months 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
Scholar 2.0 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Scholar 2.1 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Scholar 2.1 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 2.1 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance

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