Moderator: Philipp Bayer

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Philipp Bayer5.5k
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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

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Answer: A: sorting a BAM file
... That seems to be a very strange read, how can it have a MAPQ > 0? Anyway, you can either try `samtools sort -n` to sort by name, or try setting PICARD's VALIDATION_STRINGENCY to 'lenient', so for example java -jar picard.jar SortSam I=your_input O=your_sorted_output VALIDATION_STRINGENCY=L ...
written 9 hours ago by Philipp Bayer5.5k
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Comment: C: genomescope profile failed to converge
... Tell them 'congratulations' from me, it's a really cool paper! ...
written 16 days ago by Philipp Bayer5.5k
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Comment: C: genomescope profile failed to converge
... Same for me, lack of coverage so no peak, I've never seen anything else myself. There's an unlikely chance that it's a highly fragmented genome, see Suppl. Figure 3 in ['The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes'][1]. But again, unlikely. [1]: https://www ...
written 16 days ago by Philipp Bayer5.5k
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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 25 days ago by Philipp Bayer5.5k
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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 27 days ago by Philipp Bayer5.5k
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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 5 weeks ago by Philipp Bayer5.5k
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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 6 weeks ago by Philipp Bayer5.5k
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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 6 weeks ago by Philipp Bayer5.5k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Your hard-drive is full, delete unnecessary stuff :) ...
written 6 weeks ago by Philipp Bayer5.5k
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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 7 weeks ago by Philipp Bayer5.5k

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