Tag: UCSC

Bioconductor – BSgenome.Btaurus.UCSC.bosTau9.masked (development version)

DOI: 10.18129/B9.bioc.BSgenome.Btaurus.UCSC.bosTau9.masked     This is the development version of BSgenome.Btaurus.UCSC.bosTau9.masked; for the stable release version, see BSgenome.Btaurus.UCSC.bosTau9.masked. Full masked genome sequences for Bos taurus (UCSC version bosTau9) Bioconductor version: Development (3.16) Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects….

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How to modify VCF file?

Hi community, I have a question: the SNP position in vcf file is from GRCh37/hg19, I need to change the position to GRCh38. So, I used UCSC liftover to replace the hg19 pos by GRCh38 pos and deleted some SNPs, then sorted the pos and saved to a new vcf…

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extendedSequences length is not the required for DeepCpf1 (34bp)

Hi, I’m using CRISPRseek dev v. 1.35.2, installed from github (hukai916/CRISPRseek). I wanted to calculate the CFD, and the grna efficacy of a Cas12 sgRNA (my_sgrna.fa file) using Deep Cpf1. my_sgrna.fa, TTTT (PAM) + sgRNA (20bp): >sgrna1 TTTTTGTCTTTAGACTATAAGTGC Command: offTargetAnalysis(inputFilePath = “my_sgrna.fa”, format = “fasta”, header = FALSE, exportAllgRNAs =…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article  Google Scholar  Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….

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Bioconductor – BSgenome.Cjacchus.UCSC.calJac4

DOI: 10.18129/B9.bioc.BSgenome.Cjacchus.UCSC.calJac4     Full genome sequences for Callithrix jacchus (UCSC version calJac4) Bioconductor version: Release (3.15) Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation…

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downloading human rRNA.fasta

downloading human rRNA.fasta 1 I am trying to download human rRNA.fasta file. do you know where I can find this file? in one of the older post in this forum, someone said this file can be found on the UCSC but I did not manage. rRNA • 154 views •…

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Recent developments in miRNA based recombinant protein expression in CHO

Aguiar TQ, Santos SB, Martins IM, Domingues L, Oliveira C (2019) Production and bioengineering of recombinant pharmaceuticals. Proteins: sustainable source, processing and applications. Elsevier, Amsterdam, pp 259–293 Chapter  Google Scholar  Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH (2020) Inhibition of endogenous miR-23a/miR-377 in CHO cells…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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Annotated file with gene ID (instead of gene symbol)

Annotated file with gene ID (instead of gene symbol) 0 @9cb59de3 Last seen 14 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am using a gtf file in the homepage of…

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Transcription Start Site

Transcription Start Site 2 What are the best databases to check out the transcription start sites of specific genes in human genome? TSS • 130 views wget -q -O – “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz” | gunzip -c | awk ‘(int($7)< int($8)) {if($4==”+”) {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,$7,int($7)+1,$2,$4);}else {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,int($8)-3,$8,$2,$4);}}’ chr1 69090 69091 ENST00000335137.3 + chr1 139306 139309 ENST00000423372.3…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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UCSC and Amazon Web Services work to accelerate genomics research

The UC Santa Cruz Genomics Institute is collaborating with Amazon Web Services (AWS) to allow researchers to quickly and efficiently execute bioinformatics pipelines on AWS’s global cloud infrastructure. AWS and UCSC are committed to accelerating genomics research by integrating the Dockstore project, a leading repository for scientific and biomedical workflows…

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‘No genomes installed!’ error from getREF

I was trying to use the getPlotSetArray() function, but I got the error ‘No genomes installed!’ from the getREF function. I digged into the problem and it turns out that in the latest version of the BSgenome package the output of the function BSgenome::installed.genomes(splitNameParts=TRUE) changed from: pkgname organism provider provider_version…

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subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

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Difference between knownGene and wgEncodeGencodeCompV39

Hi: I am a bit confuse with the the relationship/difference between knownGene and wgEncodeGencodeCompV39 on UCSC Table Browser. Anyone know the precise difference between them? They both can be downloaded from the goldenPath page. knownGene: The schema is here, which is NOT match the file (knownGene.txt.gz) I downloaded. According to…

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South-to-north migration preceded the advent of intensive farming in the Maya region

Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS  PubMed  Google Scholar  Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS  PubMed  PubMed Central  Google Scholar  Raghavan, M. et al. Genomic evidence for…

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Bioconductor – BSgenome.Ppaniscus.UCSC.panPan1

DOI: 10.18129/B9.bioc.BSgenome.Ppaniscus.UCSC.panPan1     Full genome sequences for Pan paniscus (UCSC version panPan1) Bioconductor version: Release (3.14) Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

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Low transcript quantification with Salmon using GRCm39 annotations

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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TargetScanHuman 7.1

TargetScanHuman 7.1 * broadly conserved = conserved across most vertebrates, usually to zebrafish  conserved = conserved across most mammals, but usually not beyond placental mammals TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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[Cbseweb] Arabidopsis genome in UCSC genome browser

A question for the browser group. ———- Forwarded message ———-From: *Colaneri, Alejandro Cesar*Date: Saturday, June 16, 2012Subject: [Cbseweb] Arabidopsis genome in UCSC genome browserTo: “***@cbse.ucsc.edu” <***@soe.ucsc.edu> I was trying to use the TABLE function for the Arabidopsis genome browser epigenomics.mcdb.ucla.edu/contacts.html Do I need special permit to access to this function?…

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Bioconductor – txcutr (development version)

DOI: 10.18129/B9.bioc.txcutr     This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…

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Bioconductor – r3Cseq

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see r3Cseq. Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) Bioconductor version: 3.3 This package is an implementation of data analysis for the long-range interactions from 3C-seq assay. Author: Supat Thongjuea, MRC Molecular…

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The Difference Between Genome Reference(scRNAseq) And Transcriptome Reference(bulk RNAseq)

I want to know the difference between Genome Reference in scRNAseq and transcriptome reference in bulk RNAseq. But I didn’t get any better answer in any other place. I know we could download genome reference from UCSC, NCBI, ENSEMBL and GENECODE for bulk RNAseq. And here are the links below:…

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Bioconductor – BSgenome.Scerevisiae.UCSC.sacCer3

DOI: 10.18129/B9.bioc.BSgenome.Scerevisiae.UCSC.sacCer3     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Scerevisiae.UCSC.sacCer3. Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3) Bioconductor version: 3.10 Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects. Author: The…

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Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

There are four types of methods to extract longest transcript or longest CDS regeion with longest transcript from transcripts fasta file or GTF file. 1.Extract longest transcript from gencode transcripts fasta file. 2.Extract longest transcript from gtf format annotation file based on gencode/ensembl/ucsc database. 3.Extract longest CDS regeion with longest…

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can not upload GTF file to UCSC genomebrowser

We are unable to reproduce the error you are seeing and we also recentlyexperienced temporary issues with our site. Please let us know if youare still having this problem. Post by Gang WeiDear manager of UCSC Genome Browser,Glad to write to you. I’m now using UCSC genome browser to check…

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Bioconductor on Microsoft Azure – Microsoft Tech Community

Co-authored by: Nitesh Turaga – Scientist at Dana Farber/Harvard, Bioconductor Core Team Erdal Cosgun – Sr. Data Scientist at Microsoft Biomedical Platforms and Genomics team Vincent Carey – Professor at Harvard Medical School, Bioconductor Core Team   Introduction   The Bioconductor project promotes the statistical analysis and comprehension of current and emerging…

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How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

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Convert DNAStringSet to a list of elements in R? (Error in seq[[1]][[“seq”]] : subscript out of bounds in R)

I have a bed file which contains DNA sequences information as follow: ** track name=”194″ description=”194 methylation (sites)” color=0,60,120 useScore=1 chr1 15864 15866 FALSE 894 + chr1 534241 534243 FALSE 921 – chr1 710096 710098 FALSE 729 + chr1 714176 714178 FALSE 12 – chr1 720864 720866 FALSE 988 -…

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Annotation of alternative cattle genome assembly

University of Maryland have assembled the cattle genome and in severalways we find this to be better than the Baylor assembly. Several groups including ours are using this version ofthe assembly. ftp.cbcb.umd.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.0/ NCBI has agreed to provide annotations for this version of the assemblyalso. I request you to host this…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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hg38 Import custom reference upload error

Our version of TS is 5.12.2 When trying to upload new custom reference fasta (downloaded from ncbi ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz, gunzipped and renamed to hg38.fasta) through “Import custom reference” in interface an error occures: “uploaded file size is incorrect” (to be honest the error was not shown in logs, because of TypeError…

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“Paired-end reads were detected in single-end read library”

“Paired-end reads were detected in single-end read library” 0 @9cb59de3 Last seen 12 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am trying to use a gtf file in the homepage…

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identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

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Clinical Bioinformatics Analyst (m/w/d) – Foundation Medicine GmbH – Biology & Life Sciences

Clinical Bioinformatics Analyst (m/w/d) PENZBERG, GERMANY Foundation Medicine is leading a transformation in cancer care, where each patient’s treatment is informed by a deep understanding of the molecular changes that contribute to their disease. As a molecular information company, we are focused on fundamentally changing the way in which patients…

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Bioconductor – monaLisa

DOI: 10.18129/B9.bioc.monaLisa     Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…

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From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37?

From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37? 0 Hi all, I am trying to annotate list of genes with gene start, gene end (build37) and chromosome. I mapped most of the genes from a list downloaded from Biomart/UCSC,…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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10q26 FGFR2 Break Apart FISH Probe Kit

1 0q26 FGFR2 Break Apart FISH Probe Kit For Research Use Only Not for Use in Diagnostic Procedures 0q26 FGFR2 Break Apart FISH Probe Kit 09N /R2 Key to Symbols Used 09N /R2 Reference Number Lot Number Global Trade Item Number Centromere D0S294 0q26. Region FGFR2 5 ATE SHGC-529 Telomere…

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Bioconductor – BSgenome.Mmulatta.UCSC.rheMac10

DOI: 10.18129/B9.bioc.BSgenome.Mmulatta.UCSC.rheMac10     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Mmulatta.UCSC.rheMac10. Full genome sequences for Macaca mulatta (UCSC version rheMac10) Bioconductor version: 3.11 Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings…

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How to convert bedgraph file with bins into GRanges object?

You could convert your bedGraph bins from hg18 to hg19 using liftover, so you can overlap them with your peaks. You would read them into a GRanges object, then hand this to the liftover function to translate from hg18 to hg19, then unlist the results to get back a regular…

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40231867-SWI-Prolog-as-a-Semantic-Web-Tool-for-semantic-querying-in-Bioclipse-Integration-and-perfor – SWI-Prolog as a Semantic Web Tool for semantic

Unformatted text preview: SWI-Prolog as a Semantic Web Tool for semantic querying in Bioclipse: Integration and performance benchmarking Samuel Lampa June 2, 2010 Abstract The huge amounts of data produced in new high-throughput techniques in the life sciences, and the need for integration of heterogeneous data from disparate sources in…

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Sr Scientist – IVD Development – Houston

NuProbe USA Inc . is looking for a Staff/Senior Scientist to lead the IVD project development program at NuProbe to support both research and in vitro diagnostic (IVD) assays for use in medical research, clinical trials, regulatory submissions, and clinical diagnostic use.  NuProbe USA is a rapidly growing company and…

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transcripts are not true in TxDb.Hsapiens.UCSC.hg38.knownGene

transcripts are not true in TxDb.Hsapiens.UCSC.hg38.knownGene 1 @11b02720 Last seen 2 hours ago United States Hello, I used TxDb.Hsapiens.UCSC.hg38.knownGene/GenomicFeatures to retrieve gene promoters and other genomic features. here is code: library(‘TxDb.Hsapiens.UCSC.hg38.knownGene’) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene PR <- promoters(txdb, upstream=2000, downstream=0) but when I take a look at the PR results: it…

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Summer Intern -Bioinformatics – Roche – Pleasanton

·  Job facts Summer Intern – (Bioinformatics) The Summer @ Roche Intern Program has been developed to provide students with a fun yet rewarding summer through hands-on experience and numerous opportunities to network with other interns as well as employees in the organization. Additionally, we help our students meet their…

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Generating Multiple Species Alignment Of Novel Transcripts For Phylocsf

Short version: How would you go about generating multiple species alignments of novel transcripts from bos taurus (assembly UMD3.1) with human/mouse/dog for use with PhyloCSF? Context and what I’ve tried so far: Through a sequencing experiment, our lab has identified a large set of new transcripts in Bos taurus. We…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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Bioconductor – Rariant

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rariant. Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies Bioconductor version: 3.0 The ‘Rariant’ package identifies single nucleotide variants from sequencing data based on the difference of…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg19

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg19. Full genome sequences for Homo sapiens (UCSC version hg19) Bioconductor version: 3.2 Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. Author:…

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Bioconductor – csaw

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see csaw. ChIP-seq analysis with windows Bioconductor version: 3.2 Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. Author: Aaron Lun <alun at wehi.edu.au>,…

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Interpretting phastConsElements from USCS Table Browser

Interpretting phastConsElements from USCS Table Browser 0 I am trying to understand the information present in PhastCons elements bed files from USCS Table Browser. Following the information I found here I managed to get a description of the column names, but not a description of what they are measuring. I…

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TCGA dataset normalization

TCGA dataset normalization 0 hi. i am new to machine learning. i want to normalize my data which I downloaded from UCSC Xena browser for pancreatic cancer TCGA PAAD is its id. when I try to run this code it is showing error given below library( “DESeq2” ) library(ggplot2) countData…

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What is the codification in genestrand 1 and 2?

What is the codification in genestrand 1 and 2? 0 Hi there, I’m doing some peak annotation using ChIPseeker library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(clusterProfiler) library(annotables) library(org.Hs.eg.db) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peaks= readPeakFile(“peaks_”, header = F) peakAnno <- annotatePeak(peaks, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb=”org.Hs.eg.db”) peaks_annot <- as.data.frame(peakAnno) In my annotation file “geneStrand” is codified as…

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Bioconductor – VanillaICE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see VanillaICE. A Hidden Markov Model for high throughput genotyping arrays Bioconductor version: 3.4 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. Author: Robert Scharpf <rscharpf at jhu.edu>, Kevin Scharpf,…

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Convert UCSC isoform ID to Ensembl transcript ID

Convert UCSC isoform ID to Ensembl transcript ID 2 Hello everyone, I have a few UCSC isoform IDs and I would like to convert them to the corresponding Ensembl transcript IDs. I have tried to use some online conversion tools (such as DAVID), looked up the UCSC annotation files, but…

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Associate Director, Computational Biology/Bioinformatics Job Opening in Cambridge, MA at Obsidian Therapeutics

About Us… Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s programs apply our CytoDriveTM technology in Cell and Gene therapy products to control expression of proteins for enhanced therapeutic efficacy and safety. We’re proud of our diverse talented team and committed to…

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Database for Enhancers with Coordinates

Database for Enhancers with Coordinates 4 Can anyone recommend some good databases for extracting bed files with enhancer coordinates. I have used UCSC in the past, I was hoping to find some alternatives ChIP-Seq genome • 163 views • link updated 11 minutes ago by Papyrus &starf; 1.3k • written…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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Visulization of raw 4C-seq reads in UCSC

Visulization of raw 4C-seq reads in UCSC 1 I’m trying to create bedGraph files to view raw and normalised reads from a 4C-seq experiment to view in UCSC for two biological replicates. Is there a simple way to do this? I’ve tried using bamCoverage and expected to get peaks for…

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How to download BED file with all the fields?

How to download BED file with all the fields? 2 Hello, my goal : to download a certain BED file from ucsc website that contains all these fields: bin chrom chromStart chromEnd name score strand signalValue pValue qValue peak I will describe my actions and my problem: – I go…

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how to to download a BED file from ucsc to directory using linux

how to to download a BED file from ucsc to directory using linux 2 Hello, my goal : to download a BED file as desribed here to my directory using linux commands . in the meantine, I am trying to download the wanted file directly in the following way: my…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Bioconductor – chipseq

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chipseq. chipseq: A package for analyzing chipseq data Bioconductor version: 3.4 Tools for helping process short read data for chipseq experiments Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Bioconductor Package…

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Exon coordinates and sequence

I did it like that: 1- Download refGene.txt.gz and hg19.fasta from the UCSC goldenpath. ( note: convert hg19.2bit to hg19.fa using twoBitToFa ) 2- Create a bed file with exon coordiniate using my awk script // to_transcript.awk BEGIN { OFS =”t” } { name=$2 name2=$13 sens = $4 ==”+” ?…

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Liftover nonmodel VCF

Liftover nonmodel VCF 1 Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I’ve found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can…

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Annovar: Mouse database download

Annovar: Mouse database download 1 Hi there, I want to work with specific mouse strain from ucsc browser (A/J) on my annovar. How do I download it? perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mousedb –> is for mm10 db I have tried –> perl annotate_variation.pl -buildver 16 Strains…

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How to get enome feature annotation through NCBI api ?

How to get enome feature annotation through NCBI api ? 1 Hi, I wanna get the whole genome annotion result with some information ,like transcript,exon,gene etc , As we know ,NCBI has provided the GFF file containing the above information , but I wanna get the latest content from NCBI…

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UCSC MySQL access

UCSC MySQL access 1 Anyone know if the public can still access UCSC db remotely? Can’t seem to get access :/ genome.ucsc.edu/goldenPath/help/mysql.html XXX@XXX-MacBook-Pro:~$ mysql –user=genome –host=genome-mysql.soe.ucsc.edu -A -P 3306 ERROR 2002 (HY000): Can’t connect to MySQL server on ‘genome-mysql.soe.ucsc.edu‘ (36) XXX@XXX-MacBook-Pro:~$ mariadb –version mariadb Ver 15.1 Distrib 10.5.8-MariaDB, for osx10.15…

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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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UCSC Gene Table Exon Frames Generating Stop Codons

Hi, I’m using UCSC gene tables, and I am running into trouble with interpreting exon frames. In some cases, using the exon frame from the tables creates stop codons, which shouldn’t be happening in coding regions. As an example, from the hg19 gene NM_001369291 on chromosome 22, I have this…

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Converting between UCSC id and gene symbol with bioconductor annotation resources

You need to use the Homo.sapiens package to make that mapping. > library(Homo.sapiens) Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,…

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Bioconductor – ramr

DOI: 10.18129/B9.bioc.ramr     Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…

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How to rename the elements in columns(txdb)?

How to rename the elements in columns(txdb)? 0 Hello Biostars Community, I made a txdb object using: mm39.txdb <- makeTxDbFromEnsembl(organism = “Mus musculus”) and then made the CompressedGRangesList : txns <- GRangesList(cds(mm39.txdb, columns = c(“CDSSTART”,”CDSEND”))) I am trying to figure out how to rename CDSSTART to cdsStart and CDSEND to…

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Convert between UCSC gene id(?) and gene symbol with bioconductor

Convert between UCSC gene id(?) and gene symbol with bioconductor 0 I would like to convert between what I think are UCSC gene ids and gene symbols (see example below). I would prefer to do this with a bioconductor annotation package (org.Hs.eg.db) rather than biomart. Is “UCSC gene id” the…

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Bioconductor – TxDb.Dmelanogaster.UCSC.dm3.ensGene

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see TxDb.Dmelanogaster.UCSC.dm3.ensGene. Annotation package for the Dmelanogaster_UCSC_dm3_ensGene_TxDb object Bioconductor version: 2.9 Contains the Dmelanogaster_UCSC_dm3_ensGene_TxDb object annotation database as generated from UCSC Author: Marc Carlson Maintainer: Biocore Data Team <bioconductor at r-project.org> Citation (from within…

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Where can I get ?or how can I make a mappability track for hg38 assembly

Where can I get ?or how can I make a mappability track for hg38 assembly 2 Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use. Required tools: GEM libary from here UCSC’s wigToBigWig from here (I chose binary for Linux 64…

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UCSC knownCanonical hg19 vs. hg38

Hello, We have an FAQ page that covers this topic (genome.ucsc.edu/FAQ/FAQgenes.html#singledownload). As posted by ATpoint, it boils down to different datasets and different approaches. hg19 knownCanonical was last updated in 2013 and built primarily from RefSeq and GenBank sequences and a few other sources. One isoform was identified from each…

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List of codon numbers in a panel

List of codon numbers in a panel 1 Hello everyone!! My group sequenced multiple hotspots of a panel of genes. Now they want me to create a list with what it is sequenced, with the gene name, the exon and the codon number. I have reached the point to know…

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GenomeInfoDb (in R) and UCSC just stopped co-operating in terms of mm10

GenomeInfoDb (in R) and UCSC just stopped co-operating in terms of mm10 1 Hello, Don’t know how many have noticed but any function in GenomeInfoDb library (as well as ensembldb library) in R haven’t been able to interact with UCSC servers what comes to mm10. Typical functions like Seqinfo(genome=”mm10″) return…

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Get rsID for a list of SNPs in an entire GWAS sumstats file

Here is a fairly efficient way to do this; assuming hg38 and BEDOPS and standard Unix tools installed. $ bedmap –echo –echo-map-id –delim ‘t’ <(awk ‘{n=split($0,a,/[:_]/); print “chr”a[1]”t”a[2]”t”a[2]+1″t”a[3]”https://www.biostars.org/”a[4];}’ sumstats.txt | sort-bed -) <(wget -qO- hgdownload.cse.ucsc.edu/goldenPath/hg38/database/snp150.txt.gz | gunzip -c | cut -f2-5 | sort-bed -) > answer.bed This gets around making…

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UCSC liftover

UCSC liftover 2 Hi, I’m using UCSC liftover to convert hg19 to hg38. The result came out that I don’t understand. Feb. 2009 (GRCh37/hg19) → Dec. 2013 (GRCh38/hg38) – chr1:120904787 → chr1:143905854 Dec. 2013 (GRCh38/hg38) → Feb. 2009 (GRCh37/hg19) – chr1:143905854 → chr1:149400430 (I didn’t check “Allow multiple output regions”.)…

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How to download GTEx figure from USCS genome browser

How to download GTEx figure from USCS genome browser 1 Hello, Unfortunately the GTEx images are generated on demand then erased later. In case it helps, these are dynamically generated by R from the track data. We can help with finding the exact parameters if you are interested. The temporary…

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Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries?

Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries? 0 Hi all, On the GtRNAdb (tRNA-SE analysis) website there is a file containing fasta sequences of different tRNA genes. gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/ I aligned this GtRNAdb database with RNAseq libraries using bowtie2 and got…

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Bioinformatics Scientist in Frederick, MD

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

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Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Solvuu hiring Bioinformatics Engineer in United States

Summary At Solvuu, we are building technology to revolutionize bioinformatics and data science. We are seeking an accomplished, self-motivated and ambitious bioinformatics engineer with a strong track record in developing, executing, and maintaining bioinformatics pipelines on AWS for biotech R&D. The successful candidate will have the opportunity to drive and…

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Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

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Novogene America hiring Bioinformatics Specialist in Sacramento, California, United States

Job description Responsibilities: · Develop and maintain bioinformatics pipeline of NGS data · Research in Bioinformatics Specialty and Follow up the Frontier Trends of Life Science Research · Data mining from high throughput sequencing data generated by Novogene or other research groups. · Responsible for the maintain and improvement of…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major     Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151) Bioconductor version: Release (3.13) Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings…

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Data Brokers and Data Broker Supervisor at UCSC

Job:HIRING: Data Brokers and Data Broker Supervisor at UCSC 0 Remote Candidates Considered The Pathogen Genomics team at the Genomics Institute uses the latest sequence analysis and visualization technologies to facilitate outbreak investigation and research for public health responses. If you are excited to work in a fast-paced, startup-like environment…

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Head of Bioinformatics job in Princeton, NJ | GENMAB A/S

Genmab is focused on the creation and development of innovative and differentiated antibody products, with the aim of improving the lives of cancer patients. The Role The successful candidate will lead the global bioinformatics function and be responsible for many aspects of data including architecture, access, classification, standards, integration, pipelines…

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unable to find chromosome in SAM header

featureCounts: unable to find chromosome in SAM header 0 I am using featureCounts to try and create a count table for some RNA-Seq data I collected using an Oxford Nanopore platform. I have .sam files aligned with minimap2, and am running the following command to try to get a count…

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