Moderator: Philipp Bayer

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Philipp Bayer6.0k
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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: Problem with bedtools subtract
... This thread on the bedtools forums indicates that you're running out of memory: https://groups.google.com/forum/#!topic/bedtools-discuss/faEeLUgvb5o ...
written 27 days ago by Philipp Bayer6.0k
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... That's a Perl error - you need to install Devel::CheckLib and DBD::mysql in your Perl installation, using either cpanm or cpan - have a look at the OrthoMCL manual, the required Perl libraries should be listed there ...
written 4 weeks ago by Philipp Bayer6.0k
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Comment: C: Has anyone run Phobius locally? Error - could not read provided fasta sequences
... This fixed it for me - ./decodeanhmm would result in an error: -bash: ./decodeanhmm: No such file or directory (how is that even possible? the file is right there!), so I downloaded this copy: https://github.com/chefnb/ParseTargs/blob/master/tmhmm-2.0c/bin/decodeanhmm and tried to ru ...
written 5 weeks ago by Philipp Bayer6.0k
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Comment: C: Having trouble using wildcard
... What happens when you type ls ./temp_expt/Sample_MBM118/MBM18*_R1_001.fastq ? I reckon those files don't exist ...
written 5 weeks ago by Philipp Bayer6.0k
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Answer: A: masurca runCA failed
... Are you sure you printed the correct config file? That looks like it's trying to submit a SLURM job (`sbatch: not found`) - perhaps the default for USE_GRID is 1, and you for some reason commented that one out - it should be USE_GRID=0 (with no comments) ...
written 7 weeks ago by Philipp Bayer6.0k
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Comment: C: Some script or program to create venn diagrams for Orthofinder results?
... Hi Ivan the families.txt file you can write yourself, have a look at the example families.txt in the repository's README, or in the example_data folder. For the singletons file, that's just a list of unclustered genes: https://github.com/philippbayer/orthomclToVenn/blob/master/example_data/singleto ...
written 7 weeks ago by Philipp Bayer6.0k
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Answer: A: Some script or program to create venn diagrams for Orthofinder results?
... A while ago I wrote a script and put it onto GitHub - it's for OrthoMCL output but as far as I remember the Orthofinder Orthogroups.txt file tries to mimic OrthoMCL output https://github.com/philippbayer/orthomclToVenn Of course, with more than three sets a Venn diagram becomes messy. In that case ...
written 8 weeks ago by Philipp Bayer6.0k
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Answer: A: RNA-seq analysis data analysis piepline
... I suggest the Hisat2/Stringtie/Ballgown pipeline, see Dave Tang's blogpost: https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/ For read cleaning and adapter trimming, have a look at fastp: https://github.com/OpenGene/fastp ...
written 10 weeks ago by Philipp Bayer6.0k
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Answer: A: how remove stopcodons from a GFF
... How are you running scipio? Looking at the manual, you run scipio with your amino acid fasta file, not your gff file: scipio.1.4.pl --blat_output=prot.vs.genome.psl genome.fa proteins.aa > scipio.yaml # takes ~7m In that case, your input amino acid file has stop codons, which are normall ...
written 10 weeks ago by Philipp Bayer6.0k
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Gff3 - moving an annotation from scaffold level to pseudomolecule level
... I have an annotation for a genome assembly in scaffold format in gff3/fasta format - someone else has ordered these scaffolds into pseudomolecules, so now I want to move the 'old' annotation in gff3 format from their scaffold positions into the pseudomolecules' position. I could write a script to ...
assembly annotation written 10 weeks ago by Philipp Bayer6.0k • updated 10 weeks ago by Carambakaracho970

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