Bioconductor Forum

Hi,   Gviz is an amazing package. But I found that the junction numbers reported from sashimi plot were quite different from the junction numbers generated by “summarizeJunctions” command...from GenomicAlignments package. I got junction numbers with following codes:   \# Gviz library(Gviz) afrom<-2960000 ato<-3160000 alTrack <- AlignmentsTrack(system…

gviz genomicalignments

updated 10.0 years ago • chengwang29

for getting the observed fragment length (would need to be NA > when pairs are on different chromosomes). This should at least have an > option (if not always) to exclude the N cigar runs from the calculation. Or > it could...gt; at least in the case of gsnap excludes the Ns). From the SAM Spec: TLEN: signed observed Template LENgth. If all segments are mapped to the same …

Alignment Cancer GenomicRanges Alignment Cancer GenomicRanges

updated 13.5 years ago • Hervé Pagès

question about the CopywriteR package: 1) I have observed that CopywriteR did not detect any copy number variations (CNVs) in normal samples. Is it possible to use CopywriteR for CNV detection? 2) What’s the large gap inside...chromosome?(e.g. chr1,chr9) is this regions “blacklist”? 3) Is there any cut-off value for judging whether CNV exist or not? 4) Can I extract

copynumber cnvtools cnv copywriteR

updated 9.4 years ago • ahinsahr11

those probes without a defined position in the process. I now wish to exclude probes from the sex chromosomes before using dmpFinder, and so I am seeking to subset the GenomicMethylSet to the autosomes only. Despite days...of searching and a number of references saying this is relatively straightforward, I have not yet had any success (have been exploring GenomicRanges

Microarray Annotation PROcess minfi Microarray Annotation PROcess minfi

updated 13.0 years ago • Toby Hughes

when exporting your results to a file. Can you let me know if that explains the difference in number of transcripts you notice? Cheers, Steffen > Dear mailing list, > > I have recently observed a discrepancies in genome...package biomaRt. > I wanted to download all ensembl transcripts from the entire mouse > genome (chromosome 1:19, X, Y MT only). > &a…

biomaRt biomaRt

updated 16.2 years ago • steffen@stat.Berkeley.EDU

div class="preformatted">Dear Friends, My following geneRange object has all chromosomal information in one GRange object. library(VariantAnnotation) library(TxDb.Hsapiens.UCSC.hg19.knownGene...geneRange[i],baseUrl,geno="GT",info=NA) print(inGene) } If I have my geneRange information as per chromosome in GRangeList form, my script becomes more efficient. because, I can retrive genotypes fro…

SNP GO convert SNP GO convert

updated 12.1 years ago • Prashantha Hebbar

Hello! I am new to Gene Ontology. I have a couple of lists of common DEG's from a couple of diseases. I want to shortlist the number of genes to get candidate genes using gene ontology. I am looking for using David tool or shiny go tool for analysis. Can...I have a couple of lists of common DEG's from a couple of diseases. I want to shortlist the number of genes to get candidate genes…

microbiomeExplorer

updated 21 months ago • Bhawna

<div class="preformatted">Dear all, I was trying to visualize genes in each chromosomes in Zebrafish. I found how people visualize them in Human species using geneplotter. Then I tried followings: &gt...div class="preformatted">Dear all, I was trying to visualize genes in each chromosomes in Zebrafish. I found how people visualize them in Human species using geneplotter. Then I t…

zebrafish geneplotter zebrafish geneplotter

updated 18.6 years ago • yanju@liacs.nl

Hi, I’m running a project concerning copy number variation analysis. To run the analysis, I need to visualize the copy number data that I have. The data I have is in VCF files...fileDate=20190921 ##source=CNVkit v0.9.1.dev0 ##INFO= <id=ciend,number=2,type=integer,description="confidence around="" end="" for="" imprecise="" interval="" variants"=""> #…

copynumber plot visualization NGS gene

updated 5.1 years ago • sijing.gsj

tune segment() in DNAcopy package to generate more segments. Currently I have few segments in each chromosome (min 3 segments max-7). I want to have a least 20 segments in each chromosome. min 5 markers in each segment. also the number

DNAcopy UNDO DNAcopy UNDO

updated 14.1 years ago • Qian Liu

div class="preformatted">Hi, For a probeset, say 1010_at, its chromosome location (chr22) is 49004598-49011189. Assume the probeset has 16 PM probes, how can I get these probes' chromosome

updated 19.9 years ago • pingzhao Hu

I am seeing a significant different between my own non-integer purity/ploidy-adjusted copy number of segments and the value that PureCN reports in the LOH segments "C" column (usually integer) and I'm trying to understand...averaged over all segments of all samples, is about 0.51 copies. Since C is integer and my copy-number-adjusted values are not, I would expect the mean difference to be about…

PureC PureCN

updated 4.1 years ago • twtoal

<div class="preformatted">Dear BioC I would like to use biomaRt to get entrez gene (or other) identifiers for small tag sequences. I use the getFeature function for this. It seems that it will retrieve the identifiers only when the chromosomal region indicated spans at least the complete length of the transcript, but not if the indicated chromosomal region contains only part of the transcr…

biomaRt biomaRt

updated 18.4 years ago • Hoen, P.A.C. 't HKG

div class="preformatted">Dear list, When I used bioMart, I find a Chromosome name is HSCHR17_1. It is on chromsome 17. Why it has this name? Is there some special for this purpose? Thanks. </div

biomaRt biomaRt

updated 14.6 years ago • Fabrice Tourre

Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one... In fact 0 duplicates are found with

ChIPQC ChIPQCreport

updated 8.6 years ago • ZheFrench

Hello ... I have the following chromosome names in my hg19 reference sequence. <pre> > names(seqlengths(tx_by_gene)) [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8...Hello ... I have the following chromosome names in my hg19 reference sequence. …

reads

updated 11.2 years ago • marcovth

div class="preformatted">Hello, I would like to map some probes to their chromosome location. I am using the Affimetrix mu74a chip, so I have the Affimetrix call names like 100981_at, 93026_at, 101898_s_at...97564_f_at, 98790_s_at, etc. now I would like to know in which chromosome they are and at which distance from the centromere. Is this possible with the bioconductor package? Thanks H.Ghezzo

updated 22.5 years ago • R.Heberto Ghezzo

div class="preformatted">Hi all, Actually i am trying to make chromosome map in R for Candida albicans using *library(annotate); and library(geneplotter);*but which database i should use...in place of *hgu95av2 database which is for human chromosomal location.* Whosoever have any idea regarding my query please do reply. Any relevant reply will be appreciated

updated 16.5 years ago • ankhee dutta

rat genome assembly version 8 to align my reads in an RNA-seq experiment. When I map my gene IDs to chromosome name in biomaRt a lot of the genes are wrongly annotated (for example Ddx3y is annotated to chromosome 13 when it...should be chromosome Y, Xist is NA when it should be X, Dusp1 is NA and it should be chromosome 5, etc). This is my code: ```library(biomaRt) mart &lt

org.Rn.eg.db biomaRt

updated 19 months ago • landenshanie

<div class="preformatted">Dear all, I'm looking for a fast way of computing how many reads map into a certain location (e.g. between position 300 and 400 on chromosome 14). Is there any function to compute this in the packages chipseq or ShortRead? After reading the vignette for chipseq...way of computing how many reads map into a certain location (e.g. between position 300 and 400 on chr…

ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq

updated 16.1 years ago • Nora Rieber

div class="preformatted">Hi there, I have a number of short RNAs that have high homologies to a number of individual probes in the Medicago Affymetrix Genechip (http

gcrma gcrma

updated 19.2 years ago • Chris Dawson

div class="preformatted">Hi all, I have check some useful packages to plot gene chromosome information like gene plotter, ideogram and GenomeGraphs. However, I don't know how to plot microRNA (miRNA) chromosome...I would like to see the distribution of some miRNAs in the genome. I have known the miRNA chromosome info. miRNA name chromosome start end hsa-miR-1…

miRNA ideogram GenomeGraphs microRNA miRNA ideogram GenomeGraphs microRNA

updated 17.2 years ago • Camper Chih-Wei Liu

This command fails with the error: ``` Segmentation fault (core dumped) ``` The largest chromosome in this organism is over 2Gbp. I suspected that it may be because of these large chromosomes. To test this, I systematically...with the same error until I removed the three largest chromosomes from the SAF file. Those chromosomes have the lengths 2006429847, 1877449469 and 1725456226. Once …

Rsubread

updated 14 months ago • vkkodali

div class="preformatted">Hi. I am interested in plotting the chromosomal location of linkage markers identified in genome screens of complex diseases with differentially expressed...is it possible to label chromsome plots with centromere locations, gene symbols, p and q regions of chromosome etc. Regards Anthony -- ______________________________________________ Anthony Bosco - PhD Student …

updated 21.6 years ago • Anthony Bosco

Can I set the position of the name of the chromosome when using an IdeogramTrack? This code: <pre> transcriptID <- "ENST00000421310" chromosome <- "chr6" genome = "hg19" mart...black" ) # Create ideogram track idTrack <- Gviz::IdeogramTrack( genome = genome, chromosome = chromosome) # Set display paramters Gviz::displayPars(idTrack) <- list( …

gviz

updated 9.8 years ago • stianlagstad

Hi, is there some existing function which can use the biomart gene band information for creating chromosome plots? I've got amplification and deletion frequencies for certain genes. What I would like to do is 1. get the $band...info for a list of genes using biomart 2. make a plot for each chromosome which displays the amplification frequencies of the genes as barplot matched to a nice chromoso…

biomaRt biomaRt

updated 19.5 years ago • Benjamin Otto

div class="preformatted">Hi, I'm trying to compute the copy number for the Illumina 660W-Quad bead array with the package crlmm. But for some chromosome it doesn't work and I get the following...samples in the CrlmmSetList object were processed together in the same batch. Fitting model for copy number estimation... Using 50 df for inverse chi squares. Sufficient statistics . Estimating coeffic…

GLAD crlmm GLAD crlmm

updated 16.1 years ago • Sören Gröttrup

There are dozens of packages for working with copy number data available in Bioconductor.  However, I don’t get the sense that there is a class that unifies the somewhat standardized...processed” output that consists of: * sample\_id * <span style="line-height:1.6">chromosome</span> * start\_pos * end\_pos * copy\_number <span style="line-height:1.6">I am in…

cgh copynumber

updated 8.8 years ago • Sean Davis

sequence analysis in the chicken. I would like to use the BSgenome.Ggallus.UCSC.galGal3 package, but chromosomes 21-28 don't seem to be included. I just upgraded to version 1.3.17 of the package and 2.15.0 of R. When googling around...missing from the assembly, and that they (of course) won't be in the package either. However, the chromosomes in question are available in genome browsers, and as…

updated 13.6 years ago • Martin Johnsson

Question submitted via email: "I was wondering how X chromosome association analyses are performed by GENESIS, in particular, how are males coded and analyzed?" The answer to...Question submitted via email: "I was wondering how X chromosome association analyses are performed by GENESIS, in particular, how are males coded and analyzed?" The answer to this...on how your input data is formatte…

GENESIS

updated 5.1 years ago • Stephanie M. Gogarten

on a set of yeast genomes. Some issues: 1. sometimes some strain lacks completely a certain chromosome, hence reads counts will be zero for that chromosome. Of course I can deal with this with preprocessing, but it would...to use with this kind of samples? Especially the normalisation step is prone to fail with the whole chromosome losses I am seeing. &nbsp

cn.mops polyploidy

updated 10.2 years ago • mikko.arvas

files from different data sets. We would like to create a table of all the genomic positions per chromosome to be able to compare the samples with each other.  As the peaks found in each samples are at different chromosomal...positions, I would like to complete each chromosomes and add all the positions which have no reads with a 0. As an example this is my file: <pre> variable…

bigwig rtracklayer import granges grangeslist

updated 8.4 years ago • Assa Yeroslaviz

Hi everyone, How can I remove mitochondrial chromosome and aberrant chromosomes ("\_" pattern) from a BSgenome object? I am trying to create such object that contains only...chr1-20 and X,Y chromosomes (Rn6 genome). Thanks

bsgenome r

updated 9.6 years ago • tlgolan

Hi, I noticed a problem with biomart driven ensembl querys and it seems that the behaviour depends on the ensembl version used. I'm trying to obtain ggallus homologs for mouse genes on all autosomes and the X. With the May 2015 ensembl archive I need to query each chromosome in a loop to prevent missing genes, with the March 2015 version I can query all chromosomes at once.   <pre&…

biomart ensembl

updated 10.5 years ago • jmeisig

my Bam files using TEQC package which have been aligned on a reference with the following format chr number (1-19, X, Y ), start (integrer), end (integrer) the chromosomes are not with the prefixe chr. When I try to create the target file...Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with…

Coverage Coverage

updated 13.6 years ago • nac

when I run "genome.param" i get as output "Genome contains 5450 restriction fragments across 32 chromosomes ..." which seems to be reasonable and the number of chromosomes is right), but when I run the function that matches the...Yellow">Error in preparePairs("output.sorted.bam", genome.param, file = "test.h5",  : missing chromosomes in cut site list</span> the bam file was obt…

diffHic PreparePairs Hi-c cutGenome

updated 10.5 years ago • rulicosentino

a simple DE analysis. I would like to also pull out the differentially expressed genes and on which chromosome they are located on. How can I go about doing this? Thank you

edgeR chromosome RNAseq

updated 5.8 years ago • missmoparker

Hi all   I have a RADseq data set (from Stacks) which has no chromosome identifiers for the SNP calls. When importing the VCF file I get an error message due to this. So, I converted the...Hi all   I have a RADseq data set (from Stacks) which has no chromosome identifiers for the SNP calls. When importing the VCF file I get an error message due to this. So, I converted the "…

snprelate RADseq Stacks

updated 10.1 years ago • clive.darwell

color:Yellow">The following is the problem</span> When I ask for seqids to verify if they match the chromosome names in my BAM files I get some weird number which happens to be the NCBI chromosome accession number: <pre> head

genomicfeatures txdb canis familiaris rna-seq

updated 8.7 years ago • jggomeza

Hi, I am new to bioinformatics. I am trying to understand the meaning of chromosome column. Except for the common 22 pairs of chromosome and X, Y, some other chromosome names are strange to me like CHR

homo sapiens chromosome

updated 7.6 years ago • xchen8

plasmids and we want to focus the analysis of the effects of the experimental condition on the chromosomal genes. I was wondering if it's statistically valid to run DESeq2 on chromosome and plasmids separately or if it...s more correct running the differential expression analysis on all genes together and then analyze chromosomal and plasmids genes separately from the results. Thanks

DESeq2

updated 2.3 years ago • Laura

Does Bioconductor (or Do you provide/know about any free software programs to) analyze metaphase chromosomes, bands, and band intensities? H Leffert hleffert@ucsd.edu

genomic analysis

updated 9.2 years ago • hleffert

div class="preformatted">Hi all, I have a set of coordinates for deletions along with the chromosome. I want to show them pictorially on the chromosome. Any help appreciated. I tried using Quantsmooth package but...not able to overlay the deletion on the chromosome ideograms. Regards, -- Srinivas Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International

quantsmooth quantsmooth

updated 14.2 years ago • Srinivas Srikanth

it returns a lot of sequences that are all N's since the beginning and end of the sequenced chromosomes in the human genome contains thousands of N's. Is there any way to ignore those regions, ignore patterns that are...all N's, or trim the chromosomes to remove all the N's? Thank you very much

bsgenome matchPattern

updated 10.6 years ago • msmithmailbox

While running ChIPQC on all chromosomes it seems to enter a loop, since it finishes the computation on chromosome Y and begins again from chromosome 1...While running ChIPQC on all chromosomes it seems to enter a loop, since it finishes the computation on chromosome Y and begins again from chromosome 1. This does not happen with only one chromosome. My sessionInfo here: ``` R version 3.6.1…

chipqc chipseq ChIPQC

updated 6.3 years ago • laura.mannarino

probe ids to HGID can be obtained through the mappings to LocusLink ids to HGIDs in the homology data package. b. GO package contains new environments ANCESTOR and OFFSPRING that maps GO ids to all the ancestor...originally in GOTERM), Synonym, Secondary, Definition, and Category slots. c. homology package now maps internal HomoloGeneIds to homoData obj…

Annotation GO Organism hgu95av2 mguatlas5k mgug4121a rgug4130a probe Category Annotation

updated 21.6 years ago • John Zhang

all environments. But I have been asked to get batch-adjusted RPKM expression values for a select number of genes to make a bar chart (I of course want to use another chart type since bar charts can be deceptive) because if we

limma rna-seq removebatcheffect()

updated 7.9 years ago • Ekarl2

s "PROTEIN LIST" gives _specific_ members of enzyme families, whereas graphite seems to replace EC numbers with all family members. However, I have trouble explaining how some enzymes are on/off the list (see --- marks in the example...Example: > biocarta[["epo signaling pathway"]] "epo signaling pathway" pathway from BioCarta Number of nodes = 10 Number of edges = 24 Type of iden…

Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite

updated 13.6 years ago • Hamid Bolouri

found that there are about 8-9% of all probesets in the hgu133a package for which no information on chromosomal location (i.e. base pairs from the telomere) is available. However, other public databases like Golden Path offer...reason for this discrepancy ? What are the paths AnnBuilder uses in order to map probeset-IDs to chromosomal locations ? Would it be safe to use chromosomal locations ob…

hgu133a AnnBuilder safe hgu133a AnnBuilder safe

updated 19.5 years ago • Hilmar Berger

expressed genes from a microarray experiment. I want to to do enrichment analysis based on chromosomes. Please suggest a package or another strategy. Gaurav Bhatti [[alternative HTML version deleted]] </div

updated 15.4 years ago • Bhatti, Gaurav

fusionReadsAlignment <- Gviz::AlignmentsTrack( bamfile, isPaired = TRUE, # Setting chromosome to chrNA because this is a fusion sequence not found in # any reference genome. chromosome = "chrNA", name="Fusion Reads...fusion@genomeVersion) # This call leads to the error: Gviz::plotTracks( fusionReadsAlignment, chromosome = "chrNA", from = 1, to = nchar(fusion…

gviz

updated 8.1 years ago • stianlagstad

Gencode, by = "tx", use.names=TRUE) Where running ```seqlevels(Exons)``` outputs the names of 22 chromosomes, chrX, chrY and chrM. Perfect. However, since this is now not a ```txDB``` object, I cant use ```seqlevels(txdb) <- "chr1"``` Looking...ExonsSplitByChr <- split(Exons, seqlevels(Exons)) While I now have a list of lists for each chromosome, the slits each have ~4100 entr…

GenomicRanges split chromosome TxDb

updated 4.1 years ago • jon.klonowski

or the respective 'autoplot' function of the 'ggbio' package make it easy to visualize all the chromosomes of a genomes together. For example: autoplot(gr.snp, coord = "genome", geom = "point", aes(y = pvalue), space.skip = 0.01) ## taken...from 'example(plotGrandLinear' produces a plot for all human chromosomes with vertical lines in the middle of each chromosome. Can one easily adapt this, …

updated 11.8 years ago • Julian Gehring

downstream // 8981 // Hs.524630 // UBE2N // 7334 // ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast) /// NR_002212 // exon // 0 // --- // NUDT4P1 // 440672 // nudix (nucleoside diphosphate linked moiety X)-type motif 4 pseudogene 1 /// NM_199040...11163 // nudix (nucleoside diphosphate linked moiety X)-type motif 4 gene "NUDT4P1" is annotated on Chromosome 1 not 12 and this is only one. A…

PROcess PROcess

updated 14.0 years ago • Sebastian Thieme

27K Methylation array using the /lumi/ package. I need to associate the CpGs with the respective chromosome. Does anyone know how to integrate the information about the chromosomes in a MethyLumiM object? Many thanks in

Proteomics Proteomics

updated 14.9 years ago • Francesco Mancuso

<div class="preformatted">I may be missing something, but I don't understand the contents of the mmuhomologyLL2HGID and mmuhomologyHGID2LL environments. My understanding is that the former should take an Entrez Gene ID as a key and output a HGID number as a value, and the converse for the latter. I am trying to compare results from an experiment using Human samples to a...My understanding …

Microarray Cancer Microarray Cancer

updated 18.7 years ago • James W. MacDonald

Hi, I have BAM files (RNA-Seq data, 75 bp reads) from alignment to Zebrafish genome. I know how to plot all reads in the BAM file on each chromosomes, using gviz. However, I want to plot only the reads that do not map to any known Genes, (exons or introns), rRNA, tRNA, etc. Specifically I am interested in the reads that map to intergenic regions. I have used gviz to plot all the reads, but coul…

gviz GenomeGraphs BAM rsamtools samtools

updated 9.4 years ago • Mehmet Ilyas Cosacak

div class="preformatted">Is there R code available that maps a chromosomal position (e.g., "chr2", "80,000,000") or range (e.g., "chr2", "80,000,000 - 90,000,000") to a gene? ****************** soranim at pharmacy.ucsf.edu Marco

updated 20.5 years ago • Sorani, Marco

all of chrM SNPs get annotated as intergenic/NA (with a warning, that we ignore circular chromosomes). I can understand why that is - circular chromosomes, and a different genetic code make it trickier. Fair enough...encoded more centrally, so thought I'd ask. 2. What issues should I think about for the circular chromosomes? I'm thinking of a slightly hacky solution where I ignore any annota…

VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation

updated 11.9 years ago • Janet Young

div class="preformatted">Hi, Is there a maximum number of sequence files (chromosomes or contigs in my case) that can be fed to the forgeBSgenomeDataPkg() function? I am trying

BSgenome BSgenome genomes BSgenome BSgenome genomes

updated 12.8 years ago • Marco Blanchette