Moderator: Philipp Bayer

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Philipp Bayer4.1k
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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 • 331 results • page 1 of 34 • next >
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Answer: A: Genomestudio: The Project Can Not Be Created. No Valid Samples Were Loaded
... I just ran into this error when connecting to a Windows machine via remote desktop connection from a Linux (Fedora system). The data was stored on the Linux system while GenomeStudio ran on the Windows machine. Copying the data onto the Windows machine before loading it into GenomeStudio made this ...
written 12 hours ago by Philipp Bayer4.1k
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Answer: A: Python scripts to map multiple pair end files to the genome
... It would be easier to do this in bash: for r1 in /data/Analysis/mapped/*R1.fq do #replace R1 by R2 r2=${r1/R1/R2} # snip off the fq and add sam to the output file name out=${r1%%_R1.fq}.sam /home/yog/software/hisat2-2.0.4/hisat2 -p 8 -x /data/Analysis/Radish_ ...
written 4 days ago by Philipp Bayer4.1k
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Comment: C: Creating a dotplot from LASTZ output
... That's true, I believe LASTZ suports only one-vs-many alignments, not many-to-many ...
written 22 days ago by Philipp Bayer4.1k
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Comment: C: Creating a dotplot from LASTZ output
... I've used LAJ standalone in the past to plot LASTZ output: http://globin.bx.psu.edu/dist/laj/ Or use Symap, but then you have to rerun the alignment. ...
written 26 days ago by Philipp Bayer4.1k
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Answer: A: Get phylogenetic tree from abundance table
... There are a few tools which can give you phylogenetic trees for a list of names - phyloT, just copy paste the list of species; http://phylot.biobyte.de/ Under Python, you can use the ETEtools to download the NCBI taxonomy database and then make a tree: http://etetoolkit.org/docs/2.3/tutorial/tuto ...
written 4 weeks ago by Philipp Bayer4.1k
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Comment: C: EMBL-ABR: standards in biosciences
... In this case, 'standard' stands for an agreed upon norm around data - something like a controlled ontology (TO, GO), or even file formats (hdf5, fastq. fasta etc.) ...
written 5 weeks ago by Philipp Bayer4.1k
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Forum: EMBL-ABR: standards in biosciences
... EMBL-ABR (European Molecular Biology Laboratory Australia Bioinformatics Resource) is running a survey on the use of different standards across the data lifecycle in Australian biosciences in order to direct future efforts. If you want them to consider your experience with standards and have 10 min ...
survey standards forum written 5 weeks ago by Philipp Bayer4.1k
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Answer: A: How to delete sample using vcftools
... As it says in the [manual][1] > --indv > --remove-indv > > Specify an individual to be kept or removed from the analysis. This > option can be used multiple times to specify multiple individuals. If > both options are specified, then the "--indv" option is executed > befor ...
written 5 weeks ago by Philipp Bayer4.1k
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Comment: C: How to get non-resistance genes from PFAM families
... I'm sure that if you run Interproscan with the Pfam database on their set of resistance genes they'll all have the usual R-gene domains, copied from [this paper][1]: CC CC-NBS CC-NBS-LRR CC-TIR-NBS LRR NBS NBS-LRR TIR TIR-NBS Then you label all the remaining gen ...
written 6 weeks ago by Philipp Bayer4.1k
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Answer: A: How to get non-resistance genes from PFAM families
... I assume that they made a list of PFam domains involved in resistance (NBS-LRR etc.), then took all PFam domains that are not in that list. The paper you mentioned has no Supplementary Materials where you'd normally find these names but luckily the authors put up their negative set of non-resistanc ...
written 6 weeks ago by Philipp Bayer4.1k

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