Moderator: h.mon

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h.mon14k
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Posts by h.mon

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Comment: C: Is it possible to assess similarity between two phylo trees?
... What is the paper? It is very unlikely the authors made such claim without specifying which test they performed. ...
written 4 hours ago by h.mon14k
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Comment: C: assemble 3 SRA files for a single species
... You should convert each file separately. ...
written 4 hours ago by h.mon14k
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Answer: A: Question about Fpkm sum
... This subject is more complicated than it seems, and I will brush it slightly here, and provide further resources at the end. First, there is no reason to expect total expression of genes will be similar for different samples. There are many reasons for differences - different treatments / amounts of ...
written 12 hours ago by h.mon14k
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Answer: A: MAGMA Annotation error
... I have never run MAGMA, but just by reading you command-line, it appears to me you are swapping the arguments: >--snp-loc **NCBI37.3.gene.loc** >--gene-loc **g1000_eur.bim** Shouldn't be the other way around? --snp-loc g1000_eur.bim --gene-loc NCBI37.3.gene.loc The error message indic ...
written 12 hours ago by h.mon14k
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Comment: C: How to get million target snps info(ie. chromosome, location) in a easy way?
... Try the suggestions from the thread [Question: how to get a subset of vcf file for specific SNPs][1]. Please tell us if those work or not. If they don't, also tell us how much memory do you have available. [1]: https://www.biostars.org/p/212524/ ...
written 18 hours ago by h.mon14k
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Answer: A: Protein vs Species of Protein
... Protein species and the number of interactions are unrelated here. "Protein species" is a concept and term used in proteomics. It is fairly recent, apparently first used in [Resolution power of two-dimensional electrophoresis and identification of proteins from gels][1]. From the abstract of [this][ ...
written 19 hours ago by h.mon14k
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Answer: A: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex
... As stated above, featureCounts is faster and probably equivalent or better than HTSeq. But to answer directly your question, I will [quote][1] the author of HTSeq: >I haven't used anything else than "union" since long, and, admittedly, I would find it hard to now come up with good examples where ...
written 1 day ago by h.mon14k
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Answer: A: Biobase not running in R 3.5.0
... Check `.libPaths()`, probably the older Biobase is still installed and has precedence over the newer one. The BioConductor [install page][1] has a section on "Troubleshoot Package Installations", follow its instructions. [1]: https://www.bioconductor.org/install/ ...
written 1 day ago by h.mon14k
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Answer: A: Other genes that could account for my RNAseq reads?
... Honestly, doing the analysis again seems to me the best. You can redo everything somewhat quickly with STAR+RSEM, or you could redo **very** quickly with Salmon or kallisto. ...
written 2 days ago by h.mon14k
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Answer: A: ALLPATHS-LG denovo assembly input file pre-processing and total execution time
... You did no mistake, as far as I can see: you just don't have the mentioned library types. Warnings are not errors, and you should be able to proceed with the assembly step. (Very) approximately, I would guess at least 10 days running, but: 1) you didn't tell us your computing resources; 2) some gen ...
written 2 days ago by h.mon14k

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