Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer5.4k
Reputation:
5,390
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Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
16 hours ago
Joined:
6 years ago
Email:
p*********@googlemail.com

Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 438 results • page 1 of 44 • next >
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Comment: C: I don't know how to make this bioinformatic picture
... If your species is not in the UCSC browser, you can make very similar density plots using KaryoploteR: https://bernatgel.github.io/karyoploter_tutorial/ ...
written 9 days ago by Philipp Bayer5.4k
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Answer: A: How to circularize genome assemblies
... Yep! It's called circlator https://github.com/sanger-pathogens/circlator/wiki ...
written 28 days ago by Philipp Bayer5.4k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... You can start a new question, these have a higher likelihood of getting answered. Sounds like you still have a previous run that finished orthomclLoadBlast in the MySQL database. If you're sure that's your data then you can skip that step, I usually end up DROPping the whole database before running ...
written 28 days ago by Philipp Bayer5.4k
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Comment: C: How do you input a vcf snp file in R directly to run a PCA for the individuals?
... This previous answer will probably help you: https://www.biostars.org/p/44735/#44764 ...
written 5 weeks ago by Philipp Bayer5.4k
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Comment: C: error in orthoBlastParser
... But looking at the BLAST example output file above the 'abc|TRINITY' .. is not there, it's just 'TRINITY..'? You can rename them in the BLAST file using sed, or by rerunning BLAST ...
written 5 weeks ago by Philipp Bayer5.4k
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Answer: A: error in orthoBlastParser
... Have you run orthomclAdjustFasta on your TRINITY assembly? It doesn't look like it, it needs the '|' character everywhere, so it should be >abc|TRINITY_DN100001_c0_g1_i2.p1 >abc|TRINITY_DN100002_c0_g2_i1.p1 etc., where abc is your species shorthand of choice. ...
written 5 weeks ago by Philipp Bayer5.4k
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Comment: C: Error running smartpca from eigensoft
... Opening a new question may help , but let's try here: what is the output of echo $PATH does the list contain the folder that has smartpca? You may have to run 'export PATH' once ...
written 5 weeks ago by Philipp Bayer5.4k
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Answer: A: I always get the same Scholar Badge
... I can confirm this happens for me too since basically forever, I keep on forgetting about it ...
written 6 weeks ago by Philipp Bayer5.4k
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Job: Data Analyst, Genome Nexus. Telethon Kids Institute, Perth, Australia
... This position will develop and support bioinformatics analysis and run pipelines required for clinical and research use of next-generation sequencing (NGS) and other big data. Expertise is required to manage the bioinformatics computational platform and to assist with analysing and developing softwa ...
job perth written 7 weeks ago by Philipp Bayer5.4k
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Comment: C: Bioconductor not working through Unix command line
... >For some reason, bash thinks R is in one place, even though it also knows it's in another. I don't really get it. bash looks at the environment variable PATH, whichever comes first in PATH is used first, so if you have PATH=/usr/bin/:/home/kependleton/anaconda/bin then bash will use the s ...
written 8 weeks ago by Philipp Bayer5.4k

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
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Popular Question 5 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
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Scholar 7 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Popular Question 7 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Appreciated 8 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 9 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Scholar 10 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
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Scholar 10 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file

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