Moderator: Philipp Bayer

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Philipp Bayer5.7k
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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 • 464 results • page 1 of 47 • next >
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Answer: A: total beginner trying to learn about quality control
... Would [MultiQC][1] be fine? However, it makes a new HTML file summarising all input reports, I don't think it can make a CSV [1]: https://multiqc.info/ ...
written 10 days ago by Philipp Bayer5.7k
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Comment: C: How to run sleuth in single run mode?
... The way I understand that thread, `sleuth_live`, **not** `sleuth` now has a single library running mode - `sleuth_live` is the web server for explanatory data analysis, it doesn't do differential expression ...
written 15 days ago by Philipp Bayer5.7k
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Comment: C: How to solve ufasta error while running MaSuRCA
... Have you tried recompiling (rerunning install.sh)? Looks like ufasta is looking for GLIBC libraries that aren't there ...
written 17 days ago by Philipp Bayer5.7k
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Comment: C: FarmCPU - how to explain the reported 'effect'?
... Thank you Kevin! Yes, the coefficient makes much more sense - I'm using MVP currently which doesn't let me set `Major.allele.zero`, I will have to ask the authors! ...
written 20 days ago by Philipp Bayer5.7k
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FarmCPU - how to explain the reported 'effect'?
... When you run a GWAS using FarmCPU via GAPIT or MVP, you get an 'effect' reported per SNP (a number somewhere around -1 to +1, with a bunch of outliers). I've looked at the papers and the GAPIT forum but I'm not understanding what the effect itself reports. Is it the effect of the minor allele? The ...
gwas written 22 days ago by Philipp Bayer5.7k
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Answer: A: Getting loadings of components from pcaMethods
... Wouldn't you just need to transpose your input table while keeping names intact? tx = setNames(data.frame(t(x[,-1])), x[,1]) loadings(pca(tx, method="nipals", nPcs=2)) ...
written 23 days ago by Philipp Bayer5.7k
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Answer: A: How to add help function in a snakemake file
... Maybe [this older tutorial and its answers][1] can help you? [1]: https://www.biostars.org/p/220268/ ...
written 4 weeks ago by Philipp Bayer5.7k
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Answer: A: Cuffmerge and cuffdiff error
... What's in your assemblies.txt? I have a hunch that your original RNASeq alignments never finished, as all of your software complains about missing end-of-file markers. You can check your input bam files using samtools view your_alignment.bam > /dev/null if it still complains about EOF miss ...
written 4 weeks ago by Philipp Bayer5.7k
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Answer: A: is there a faster way to download large sequencing data from NCBI?
... I've made very good experiences with ascp instead of regular FTP The NCBI book will tell you where to download it and how to set it up: https://www.ncbi.nlm.nih.gov/books/NBK158899/ ...
written 4 weeks ago by Philipp Bayer5.7k
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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 6 weeks ago by Philipp Bayer5.7k

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