Moderator: Philipp Bayer

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Philipp Bayer5.6k
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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 • 453 results • page 1 of 46 • next >
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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 11 hours ago by Philipp Bayer5.6k
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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 8 days ago by Philipp Bayer5.6k
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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 16 days ago by Philipp Bayer5.6k
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Answer: A: fastx_collapser: Invalid quality score value (char '/' ord 47 quality value -17)
... Another suggestion: Run Trimmomatic on your data with the TOPHRED33 flag, see whether that'll change your quality scores. ...
written 5 weeks ago by Philipp Bayer5.6k
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Answer: A: Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu
... 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 6 weeks ago by Philipp Bayer5.6k
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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 8 weeks ago by Philipp Bayer5.6k
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Comment: C: genomescope profile failed to converge
... Tell them 'congratulations' from me, it's a really cool paper! ...
written 10 weeks ago by Philipp Bayer5.6k
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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 10 weeks ago by Philipp Bayer5.6k
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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 11 weeks ago by Philipp Bayer5.6k
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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 12 weeks ago by Philipp Bayer5.6k

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