Aligned RNA-seq data to ranked list of genes
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@paulig2001yahoocouk-4098
Last seen 10.3 years ago
Hello, I've got aligned rna-seq data (aligned using MAQ) for a sample and want to turn it into a list of genes ranked by their expression level in that sample. I'm wondering if anybody can point me towards a tutorial or a package that would allow me to do this? Thanks a bunch. Paul [[alternative HTML version deleted]]
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@kasper-daniel-hansen-2979
Last seen 18 months ago
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One possibility is Genominator which uses an SQLite backend for storing the data and does require a bit of time in setting up the data, but you can also do a pipeline entirely in R using IRanges/GenomicRanges and ShortRead. Kasper On Tue, May 25, 2010 at 11:22 AM, <paulig2001 at="" yahoo.co.uk=""> wrote: > Hello, > > I've got aligned rna-seq data (aligned using MAQ) for a sample and want to turn it into a list of genes ranked by their expression level in that sample. I'm wondering if anybody can point me towards a tutorial or a package that would allow me to do this? > > Thanks a bunch. > > Paul > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi All My problem is that I need to install HuEx10stv2cdf R package, but I don't know how. I found several zip file for that, but it does not work, it has this error > utils:::menuInstallLocal() Error in gzfile(file, "r") : cannot open the connection In addition: Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In gzfile(file, "r") : cannot open compressed file 'huex10stv2cdf_1.15.0.tar.gz/DESCRIPTION', probable reason 'No such file or directory' > the problem is that I want to do normalization for exon arrays and the probe names do not match with the ones from U133A for example. So, I need to make sure that the names are ok. could you please help me. Thanks very much. Best Leila > One possibility is Genominator which uses an SQLite backend for > storing the data and does require a bit of time in setting up the > data, but you can also do a pipeline entirely in R using > IRanges/GenomicRanges and ShortRead. > > Kasper > > On Tue, May 25, 2010 at 11:22 AM, <paulig2001 at="" yahoo.co.uk=""> wrote: >> Hello, >> >> I've got aligned rna-seq data (aligned using MAQ) for a sample and want >> to turn it into a list of genes ranked by their expression level in that >> sample. I'm wondering if anybody can point me towards a tutorial or a >> package that would allow me to do this? >> >> Thanks a bunch. >> >> Paul >> >> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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That's not how you install packages. Use biocLite(): http://www.bioconductor.org/docs/install/ L. Mohammadi wrote: > Hi All > > My problem is that I need to install > HuEx10stv2cdf R package, but I don't know how. > I found several zip file for that, but it does not work, it has this error > >> utils:::menuInstallLocal() > Error in gzfile(file, "r") : cannot open the connection > In addition: Warning messages: > 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 2: In gzfile(file, "r") : > cannot open compressed file 'huex10stv2cdf_1.15.0.tar.gz/DESCRIPTION', > probable reason 'No such file or directory' > > > the problem is that I want to do normalization for exon arrays and the > probe names do not match with the ones from U133A for example. So, I need > to make sure that the names are ok. > > could you please help me. Thanks very much. > > Best > Leila > > > >> One possibility is Genominator which uses an SQLite backend for >> storing the data and does require a bit of time in setting up the >> data, but you can also do a pipeline entirely in R using >> IRanges/GenomicRanges and ShortRead. >> >> Kasper >> >> On Tue, May 25, 2010 at 11:22 AM, <paulig2001 at="" yahoo.co.uk=""> wrote: >>> Hello, >>> >>> I've got aligned rna-seq data (aligned using MAQ) for a sample and want >>> to turn it into a list of genes ranked by their expression level in that >>> sample. I'm wondering if anybody can point me towards a tutorial or a >>> package that would allow me to do this? >>> >>> Thanks a bunch. >>> >>> Paul >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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My other question is how I can get a bioconductor account. I tried but I couldn't do it. thanks Leila > One possibility is Genominator which uses an SQLite backend for > storing the data and does require a bit of time in setting up the > data, but you can also do a pipeline entirely in R using > IRanges/GenomicRanges and ShortRead. > > Kasper > > On Tue, May 25, 2010 at 11:22 AM, <paulig2001 at="" yahoo.co.uk=""> wrote: >> Hello, >> >> I've got aligned rna-seq data (aligned using MAQ) for a sample and want >> to turn it into a list of genes ranked by their expression level in that >> sample. I'm wondering if anybody can point me towards a tutorial or a >> package that would allow me to do this? >> >> Thanks a bunch. >> >> Paul >> >> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Paul a relatively lightweight and reasonably fast possibility is described here: http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour Best wishes Wolfgang Kasper Daniel Hansen scripsit 25/05/10 18:26: > One possibility is Genominator which uses an SQLite backend for > storing the data and does require a bit of time in setting up the > data, but you can also do a pipeline entirely in R using > IRanges/GenomicRanges and ShortRead. > > Kasper > > On Tue, May 25, 2010 at 11:22 AM,<paulig2001 at="" yahoo.co.uk=""> wrote: >> Hello, >> >> I've got aligned rna-seq data (aligned using MAQ) for a sample and want to turn it into a list of genes ranked by their expression level in that sample. I'm wondering if anybody can point me towards a tutorial or a package that would allow me to do this? >> >> Thanks a bunch. >> >> Paul >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Also, you may want to take a look at the Vignette of the GenomicRanges package: http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html The package is particularly useful if you aligned your reads against a genomic reference. A very short code sample is given here: http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq-Analysis If you aligned your reads against a transcriptome reference then things are even easier. All you need is the ShortRead package. A short use case is available here: http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq- Profiling-Exercise Thomas On Thu, May 27, 2010 at 06:14:03PM +0200, Wolfgang Huber wrote: > Paul > > a relatively lightweight and reasonably fast possibility is described > here: http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour > > Best wishes > Wolfgang > > > > Kasper Daniel Hansen scripsit 25/05/10 18:26: > >One possibility is Genominator which uses an SQLite backend for > >storing the data and does require a bit of time in setting up the > >data, but you can also do a pipeline entirely in R using > >IRanges/GenomicRanges and ShortRead. > > > >Kasper > > > >On Tue, May 25, 2010 at 11:22 AM,<paulig2001 at="" yahoo.co.uk=""> wrote: > >>Hello, > >> > >>I've got aligned rna-seq data (aligned using MAQ) for a sample and want > >>to turn it into a list of genes ranked by their expression level in that > >>sample. I'm wondering if anybody can point me towards a tutorial or a > >>package that would allow me to do this? > >> > >>Thanks a bunch. > >> > >>Paul > >> > >> > >> > >> > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor at stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >>Search the archives: > >>http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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