User: jma1991

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jma199130
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Posts by jma1991

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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Sorry, so are you saying OCT4/POU5F1 has transcripts on different chromosomes? ...
written 8 weeks ago by jma199130
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Actually I'm a bit confused now.. Neither the gene symbol or alias returns the canonical OCT4/POU5F1 gene: library("org.Hs.eg.db") library("TxDb.Hsapiens.UCSC.hg19.knownGene") genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) symbols <- mapIds(org.Hs.eg.db, keys = genes$gene_id, "SYMBOL", k ...
written 8 weeks ago by jma199130
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Answer: A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... It's called POU5F1B instead of POU5F1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes <- genes(txdb) library("AnnotationDbi") library("org.Hs.eg.db") gene_symbol <- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, columns=" ...
written 8 weeks ago by jma199130
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Comment: C: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
... Ah that makes sense, thank you for replying ...
written 6 months ago by jma199130
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Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
... :: I originally posted my question on Biostars, but according to the featureCounts website, I should post on this forum for help :: I am using featureCounts (version 1.5.2) to count the number of reads within bins along the genome: featureCounts -R -F SAF --fracOverlap 1 -Q 1 --primary -T 20 ...
featurecounts subread written 6 months ago by jma199130 • updated 6 months ago by Wei Shi2.7k
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Comment: C: strsplit method for DNAStringSet objects
... That's fantastic, thank you very much. I'll test when it becomes available. ...
written 7 months ago by jma199130
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Comment: C: strsplit method for DNAStringSet objects
... Ah so simple, silly me. Thanks for the answer. ...
written 7 months ago by jma199130
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strsplit method for DNAStringSet objects
... Is there a strsplit method for DNAStringSet objects? I have a DNAStringSet object generated from the readFastq function (ShortRead package). In the middle of my reads is a barcode which I would like to use to split the reads into two reads (effectively treating the split read as paired-end reads). ...
biostrings shortread written 7 months ago by jma199130 • updated 7 months ago by Hervé Pagès ♦♦ 13k
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Data grouping with DataTrack or AlignmentTrack classes
... I am using Gviz to view ChIP-seq coverage from either BAM files or bigWig files. I would like to group the data by a factor variable (as described on page 21 of the Gviz user guide). However, grouping only seems to work if I pass in a matrix of data values. It doesn't work when I pass in a list of D ...
gviz gviz-package written 8 months ago by jma199130
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Hill in P-value distribution for heterogenous ChIP-seq samples
... I have data from a variant of ChIP-seq and would like to call "peaks" from the data by finding differential-binding between my ChIP samples and the paired input samples. I'm currently using the csaw workflow outlined in the excellent F1000 paper. However, I've encountered a few problems when applyin ...
limma edger sva csaw qsmooth written 9 months ago by jma199130 • updated 9 months ago by Aaron Lun17k

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