Moderator: Philipp Bayer

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Philipp Bayer5.7k
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PhilippBayer
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 455 results • page 2 of 46 • next >
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Answer: A: fasta to gff3
... There are numerous sources for gff3 files, it always depends on which organism you work with - Ensembl has many annotations in gff3 files, one example: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index I'm not sure I understand your second question. A fasta file contains a whole genome asse ...
written 3 months ago by Philipp Bayer5.7k
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Answer: A: Genome assembly and annotation
... There are many 'best practises' papers by now, the exact paper depends on your species (bacterium? plant?) and your technology (2nd generation? 3rd generation? Hybrid? 10x?) Ten steps to get started in Genome Assembly and Annotation https://f1000research.com/articles/7-148/v1 A beginner’s guide to ...
written 3 months ago by Philipp Bayer5.7k
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Answer: A: Links for forums or discussion groups about machine learning, aging, genomics an
... I think the fast.ai community is the nicest one (but very few bioinformaticians from what I saw) http://forums.fast.ai/ Their course is the best one I've seen on machine learning but very video-based which may not work for you, not sure! ...
written 4 months ago by Philipp Bayer5.7k
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Answer: A: agriGO no longer available?
... I guess they turned off agriGO v1 (yours, paper from 2010) and left only agriGO v2 (paper from 2017) up? http://systemsbiology.cau.edu.cn/agriGOv2/ Especially for GO annotation I would always use the newest data possible - see for example https://www.nature.com/articles/s41598-018-23395-2 ...
written 4 months ago by Philipp Bayer5.7k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... You can use df -h to see how much space you have left on each device. There's a chance that the mysql process is not allowed to write to the folder with 613G, so look at the rights of that folder using `ls -lah` ...
written 4 months ago by Philipp Bayer5.7k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Your hard-drive is full, delete unnecessary stuff :) ...
written 4 months ago by Philipp Bayer5.7k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... The name of one or more genes are too long for the database! Two ways to fix this: - write a small script (using Bopython or Bioperl) that cuts off the names of your IDs to below 60 characters - in the OrthoMCL script orthomclInstallSchema, change these two lines: QUERY_ID ...
written 4 months ago by Philipp Bayer5.7k
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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 5 months ago by Philipp Bayer5.7k
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Answer: A: How to circularize genome assemblies
... Yep! It's called circlator https://github.com/sanger-pathogens/circlator/wiki ...
written 5 months ago by Philipp Bayer5.7k
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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 5 months ago by Philipp Bayer5.7k

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