User: thackl

gravatar for thackl
thackl2.3k
Reputation:
2,320
Status:
Trusted
Location:
European Union
Last seen:
1 day, 9 hours ago
Joined:
2 years, 9 months ago
Email:
t*****@lim4.de

Posts by thackl

<prev • 217 results • page 1 of 22 • next >
0
votes
3
answers
393
views
3
answers
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 8 months ago by thackl2.3k
1
vote
2
answers
403
views
2
answers
Comment: C: ALLPATHS-LG slow ... multi threads possible ?
... What was your solution?? Up to 5TB for 3Gbp plant genome. ...
written 10 months ago by thackl2.3k
0
votes
2
answers
337
views
2
answers
Comment: C: Is there a term for a genome assembly that is not closed?
... And technically, even a draft assembly can be closed :) ...
written 10 months ago by thackl2.3k
0
votes
2
answers
337
views
2
answers
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 10 months ago by thackl2.3k
0
votes
2
answers
403
views
2
answers
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 10 months ago by thackl2.3k
0
votes
2
answers
403
views
2
answers
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 10 months ago by thackl2.3k
0
votes
2
answers
403
views
2
answers
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 10 months ago by thackl2.3k
2
votes
1
answer
360
views
1
answers
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 12 months ago by thackl2.3k
0
votes
2
answers
581
views
2
answers
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 13 months ago by thackl2.3k
0
votes
2
answers
703
views
2
answers
Answer: A: Salmon/Sailfish for repeat element quantification?
... In general I like the idea - and actually I used similar approaches myself to at least assess repeat copy numbers etc.. A major problem, however, is that the consensus repeat sequences often represent clusters with some sequences of only about 75%-85% identity. Transcriptome quantification methods ( ...
written 16 months ago by thackl2.3k

Latest awards to thackl

Popular Question 9 weeks ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 7 months ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 15 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 17 months ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
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
Appreciated 20 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 20 months ago, created an answer with at least 3 up-votes. 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
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Teacher 22 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
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Scholar 22 months ago, created an answer that has been accepted. 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
Appreciated 22 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Scholar 22 months ago, created an answer that has been accepted. 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
Teacher 23 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
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 701 users visited in the last hour