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Question: Elephant shark genome
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3.6 years ago by
Guest User12k
Guest User12k wrote:
Is there going to be the elephant shark (Callorhinchus milii) genome, a model cartilaginous fish, stored in Biostrings objects, like other model genomes. Thank you -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 3.6 years ago by Martin Morgan ♦♦ 20k • written 3.6 years ago by Guest User12k
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gravatar for Martin Morgan
3.6 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
On 04/23/2014 03:06 AM, Miguel [guest] wrote: > > Is there going to be the elephant shark (Callorhinchus milii) genome, a model cartilaginous fish, stored in Biostrings objects, like other model genomes. > Hi Miguel -- not sure what your use case is, can you provide some context? If you're just looking for fast access to the sequence data using Bioconductor tools you could 1. download the fasta files, maybe (are these what you're looking for??) wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_othe r/Callorhinchus_milii/Callorhinchus_milii-6.1.3/Primary_Assembly/unpla ced_scaffolds/FASTA/unplaced.scaf.fa.gz 2. In R, re-compress and index the file library(Rsamtools) fa = razip("unplaced.scaf.fa.gz") indexFa(fa) 3. Use, e.g., > fafile = FaFile("unplaced.scaf.fa.rz") > seqinfo(fafile) Seqinfo of length 21203 seqnames seqlengths isCircular genome gi|564982704|gb|KI635855.1| 18507834 <na> <na> gi|564982701|gb|KI635856.1| 17031706 <na> <na> gi|564982698|gb|KI635857.1| 16461339 <na> <na> gi|564982691|gb|KI635858.1| 16433419 <na> <na> gi|564982688|gb|KI635859.1| 15003573 <na> <na> ... ... ... ... gi|564405817|gb|AAVX02067416.1| 247 <na> <na> gi|564405816|gb|AAVX02067417.1| 234 <na> <na> gi|564405815|gb|AAVX02067418.1| 218 <na> <na> gi|564405814|gb|AAVX02067419.1| 173 <na> <na> gi|564405813|gb|AAVX02067420.1| 66 <na> <na> > idx = c("gi|564982701|gb|KI635856.1|", "gi|564982688|gb|KI635859.1|") > which = as(seqinfo(fafile)[idx], "GRanges") > getSeq(fafile, which) A DNAStringSet instance of length 2 width seq names [1] 17031706 TATAACTGGAGTGTATGTATAC...TGTACCGCCCGGGGTGGTGCG gi|564982701|gb|K... [2] 15003573 AGAGAGAGATAGAGAGAGACAG...TTGATCATGTCAACCCCCCCA gi|564982688|gb|K... There is also the vignette on creating a BSgenome package http://bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/ doc/BSgenomeForge.pdf Martin > Thank you > > -- output of sessionInfo(): > > R version 2.14.1 (2011-12-22) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 3.6 years ago by Martin Morgan ♦♦ 20k
Dear Dario, In our experiments from both simulated and real RNASeq data (under review in Bioinformatics), we have found that deseq normalization followed by the vst transformation improves the performance of classifiers, mostly for SVM and PLDA (poisson linear discriminant analysis). For the voom transformation, MLSeq currently uses the cpm values. The name of this argument will be updated as ?voom-cpm? instead of ?voom?. Yes, specialized classification and clustering algorithms are needed to combine the cpm values and voom weights. But at this moment, deseq+vst+traditional classifiers or tmm+voom-cpm+traditional classifiers are the current solutions for RNASeq based gene-expression classification. Best, Gokmen Zararsiz On Apr 23, 2014, at 12:27 AM, Bernd Klaus <bernd.klaus at="" embl.de=""> wrote: Dear Dario, I think you are right about being careful to simply use the voom weights to pre-transform the data. As Dr. Smyth pointed out a while ago, an algorithm should always use these weights explicitly in some way rather than using them to pretransform the data. You could possibly incorporate them easily in a DDA classifier for example. Apart from Wolfgangs links, I might point you to two interesting papers Zwiener et. al. - Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures [1] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.008 5150 They investigate a couple of pretransformations for RNA-Seq data classification and find that rank based transformation perform well in general. (They do not consider voom weights) [2] Gallopin et.al. - A Hierarchical Poisson Log-Normal Model for Network Inference from RNA Sequencing Data http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.007 7503 They use a GLMM combined with a lasso penalty to incorporate unequal sample variances and then estimate a graphical model using a type of partial correlation. This is somewhat similar to the voom approach, however the variances and the model parameters are estimated in "one-go". However, they note that the algorithm used is very slow. Best wishes, Bernd On Apr 23, 2014, at 9:43 AM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Dear Dario > > good points, and as usual in machine learning, I don?t expect there to be a simple answer or universally best solution. > For classification, the (pre)selection of features (genes) used is probably more important than most other choices, esp. if the classification task is simple and can be driven by a few genes. For clustering, similar, plus the choice of distance metric or embedding. > > That said, it is plausible that both, using the untransformed counts (or RPKMs etc.), or the log-transformed values, have problems with high variance (either at the upper or lower end of the dynamic range) that can be avoided with a different transformation, log-like for high values, linear-like for low (e.g. DESeq2?s vst, rlog). Paul McMurdie and Susan Holmes have some on this in their waste-not-want-not paper [1], and Mike in a Supplement to the DESeq2 paper (draft). It would be interesting to collect more examples, and someone should probably study this more systematically (if they aren?t already.) > > Kind regards > Wolfgang > > > [1] http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjourn al.pcbi.1003531 > [2 http://www-huber.embl.de/DESeq2paper ?> Regularized logarithm for sample clustering (As of today, there is a version of 19 February which I think will soon be updated with a more extensive survey). > > > > > Il giorno 23 Apr 2014, alle ore 07:00, Dario Strbenac <dstr7320 at="" uni.sydney.edu.au=""> ha scritto: > >> Hello, >> >>> From reading the vignette, MLSeq seems to be a set of wrapper functions that allows the user easy access to normalisation strategies in edgeR or DEseq and passes the data onto algorithms such as Support Vector Machine or Random Forest. Are there any results that demonstrate that normalisation improves classification performance ? I am also not convinced about the description of using voom weights to transform the data. The author of voom stated that specialised clustering and classification algorithms are needed to handle the CPM and weights separately. Why does MLSeq use standard classification algorithms and how were the weights and expression values combined ? >> >> -------------------------------------- >> Dario Strbenac >> PhD Student >> University of Sydney >> Camperdown NSW 2050 >> Australia >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 3.6 years ago by gokmenzararsiz@erciyes.edu.tr20
Thanks for the various advice. I will read the recommended articles. I'm glad there is an article about this under review. It wasn't clear in the vignette where the advice came from, but I feel confident using MLSeq now. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia
ADD REPLYlink written 3.6 years ago by Dario Strbenac1.4k
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