Moderator: Philipp Bayer
Philipp Bayer ♦ 5.7k
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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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Comment:
C: VCF input for KaryotypeR
... >however when I try to convert this to a GRanges object (which I believe is needed for karyotypeR, it does not work.
What is the exact error you're seeing? Can you give an example row from your vcf? That example data you have there doesn't look like a vcf ...
written 7 days ago by
Philipp Bayer ♦ 5.7k
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... Mick Watson came up with this simple test for bacterial genomes: http://www.opiniomics.org/a-simple-test-for-uncorrected-insertions-and-deletions-indels-in-bacterial-genomes/
With an N50 of 4,000,000 I don't expect you to have a bacterial genome :) However I don't see why this simple test wouldn't ...
written 27 days ago by
Philipp Bayer ♦ 5.7k
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Comment:
C: MCScanX empty collinearity file.
... You should have an 'edit' button where you can delete the whole question - but to answer your question, it looks like there's something wrong with the alignments file, the tandem duplications file worked fine but the inter-species comparison is broken, perhaps because the IDs in the gff file are dif ...
written 28 days ago by
Philipp Bayer ♦ 5.7k
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Comment:
C: Visualizing contig alignment
... I usually remove small contigs (<10kb) because these will only add chaos to the graph anyway. ...
written 5 weeks ago by
Philipp Bayer ♦ 5.7k
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Answer:
A: Visualizing contig alignment
... Are dotplots not an option?
Minidot is very fast, but in my experience doesn't work that great with 'bad' assemblies: https://github.com/thackl/minidot
Symap is a bit older and slower, but works better with low quality assemblies (again, in my experience), and can also make a circular plot http:// ...
written 6 weeks ago by
Philipp Bayer ♦ 5.7k
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... Another suggestion:
Run Trimmomatic on your data with the TOPHRED33 flag, see whether that'll change your quality scores. ...
written 9 weeks ago by
Philipp Bayer ♦ 5.7k
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... Things I would try:
- check whether the input file is broken (use `tail` to check the end)
- remove small contigs from the assembly (for example, `bioawk -c fastx '{ if(length($seq) > 1000) { print ">"$name; print $seq }}' sandalnew.fa > filtered_sandalnew.fa` )
- recompile augustus via ...
written 10 weeks ago by
Philipp Bayer ♦ 5.7k
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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 12 weeks ago by
Philipp Bayer ♦ 5.7k
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... Tell them 'congratulations' from me, it's a really cool paper! ...
written 3 months ago by
Philipp Bayer ♦ 5.7k
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... 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 3 months ago by
Philipp Bayer ♦ 5.7k
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