Moderator: Philipp Bayer
Philipp Bayer ♦ 6.0k
- Reputation:
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- PhilippBayer
- Last seen:
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- Joined:
- 7 years ago
- Email:
- p*********@googlemail.com
Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
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... 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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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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 Bayer ♦ 6.0k
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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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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... 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 Bayer ♦ 6.0k
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... 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 ...
written 10 weeks ago by
Philipp Bayer ♦ 6.0k
• updated
10 weeks ago by
Carambakaracho • 970
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