help with mapping statistics summary
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@lcarvalhbtkfi-5223
Last seen 10.2 years ago
Hi, I am pretty new using the bioconductor and I have some RNAseq data on which I had performed and TopHat and I need to perform a mapping summary statistics from the results. I have a pretty large BAM file of accepted hits (aprox. 17GB). I?ve been looking at the bioconductor packages and I found the Rsamtools, that I think maybe I can used to this propose, but can anyone give me any suggestion of some other package or how could I do this statistics summary? BR, Leonor
RNASeq RNASeq • 907 views
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@martin-morgan-1513
Last seen 3 months ago
United States
On 05/22/2012 01:31 AM, Leonor Carvalho wrote: > Hi, > > I am pretty new using the bioconductor and I have some RNAseq data on which I > had performed and TopHat and I need to perform a mapping summary statistics > from the results. I have a pretty large BAM file of accepted hits (aprox. > 17GB). > > I?ve been looking at the bioconductor packages and I found the Rsamtools, that I > think maybe I can used to this propose, but can anyone give me any suggestion > of some other package or how could I do this statistics summary? EDASeq from this page http://bioconductor.org/packages/release/BiocViews.html#___HighThrough putSequencing including its vignette might provide some inspiration, perhaps in conjunction with Rsamtools::scanBam or Rsamtools::readBamGappedAlignments. Use ScanBamParam(which=GRanges(<...>)) to read in part of a file if memory is an issue. Martin > > BR, > > Leonor > > _______________________________________________ > 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: M1-B861 Telephone: 206 667-2793
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Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 11 weeks ago
Australia/Melbourne/Olivia Newton-John …
No matter which package you use, you got to be aware that many junction reads are reported multiple times by TopHat if you ran TopHat with the default setting. W On May 22, 2012, at 6:31 PM, Leonor Carvalho wrote: > Hi, > > I am pretty new using the bioconductor and I have some RNAseq data on which I > had performed and TopHat and I need to perform a mapping summary statistics > from the results. I have a pretty large BAM file of accepted hits (aprox. > 17GB). > > I?ve been looking at the bioconductor packages and I found the Rsamtools, that I > think maybe I can used to this propose, but can anyone give me any suggestion > of some other package or how could I do this statistics summary? > > BR, > > Leonor > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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Hi, The main option in R is currently easyRNASeq http://www.bioconductor.org/packages/devel/bioc/html/easyRNASeq.html which is a front-end to DESeq (or edgeR), two of the most popular RNASeq packages. This is especially helpful for comparing samples with each other and handling replicates. If you've run tophat, you could use cuffdiff / cufflinks to get normalized transcript counts, as well (but this is not related to R/Bioconductor). Best, Kemal [[alternative HTML version deleted]]
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