User: goldberg.jm

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Posts by goldberg.jm

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Comment: C: RNA-seq read alignment best practices for low-input samples
... Yeah, you're right! Thanks for the suggestions on where to ask this. ...
written 4 months ago by goldberg.jm0
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RNA-seq read alignment best practices for low-input samples
... RNA-seq read alignment best practices for low-input samples Hi All, There are many ways to align RNA-seq reads to transcripts and genomes, and I am confused about which is best for my experiment. My goal is to do differential expression analysis on Plasmodium vivax data. The input is fastq files ...
alignment limma differential gene expression rsem rnaseq analysis written 4 months ago by goldberg.jm0 • updated 4 months ago by Aaron Lun19k
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Comment: C: Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refs
... In theory TXID/TXNAM - ENST mappings should be 1-to-1, right? Do you know why they are not? ...
written 16 months ago by goldberg.jm0
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Comment: C: Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refs
... Thank you... works like a charm! I really do want TXID-ENST pairings but it's good to see other examples as well. ...
written 16 months ago by goldberg.jm0
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Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
... Hi All, How do I map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript IDs or Refseq IDs?  I know this must be a basic task, but I have been playing around with it and googling all afternoon and have not cracked it. I am sure Valerie Obenchain and many others can answer this easily. ...
annotationdbi written 16 months ago by goldberg.jm0 • updated 16 months ago by James W. MacDonald46k
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select negative control probes with GEOquery
... Hi All, Using GEOquery and MBCB, I would like to background correct raw data from an experiment on the GPL10558 platform. Normalized data and metadata were got using gset <- getGEO(accession,GSEMatrix =TRUE). Raw data were got using getGEOSuppFiles(accession,baseDir = base_directory) followed by ...
limma geoquery mbcb written 2.2 years ago by goldberg.jm0

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