User: tangming2005

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tangming2005150
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Posts by tangming2005

<prev • 118 results • page 2 of 12 • next >
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unlist a exons GRangeslist object and add a gene name column
... Hi, I can not find  a way to do it. exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene") unlist(exons) # this will lost the gene name information. How do I add the name of the gene for the exons? I have read https://www.biostars.org/p/101513/ and https://support.bioconductor.or ...
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene written 2.0 years ago by tangming2005150 • updated 2.0 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi James, thanks very much for this detailed answer. now I remember a related question you answered me some time ago https://support.bioconductor.org/p/88725/#88767 again, your help is much appreciated. learned a lot! Tommy ...
written 2.1 years ago by tangming2005150
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... thanks. looks like I can not find DAXX, HLA-A, SHOX and TRIM27 in TxDb.Hsapiens.UCSC.hg19.knownGene even using the other names. but POU5F1B is not shown either AnnotationDbi::select(org.Hs.eg.db, c("POU5F1", "DAXX", "HLA-A","SHOX","TRIM27"), keytype = "SYMBOL", columns = "ALIAS") 'select()' ret ...
written 2.1 years ago by tangming2005150
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Thanks! I have a list of genes which I can not find in the txdb. DAXX, HLA-A, SHOX and TRIM27. where can I find the alternative names? Tommy   ...
written 2.1 years ago by tangming2005150
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POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi, I was trying to get the coordinates of some genes, and was surprised that POU5F1 gene is not in the txdb. Thank you for looking into this. Tommy library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes<- genes(txdb) library(AnnotationDbi) libra ...
txdb.hsapiens.ucsc.hg19.knowngene written 2.1 years ago by tangming2005150 • updated 2.1 years ago by jma199130
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... samtools view -F 256 will remove some reads, but not all not uniquely mapped reads. Have you tried TEQC on any BWA-MEM aligned bam files? from Heng Li: https://www.biostars.org/p/59281/#59303 Eland is probably the first short read aligner. It reports a tag, which can be '[UR][0-2]|NM', for each r ...
written 2.3 years ago by tangming2005150
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... I was using 3.1.0. A side question is how TEQC determine the not uniquely mapped reads for BWA-MEM aligned bam files. I read here: https://www.biostars.org/p/76893/   https://www.biostars.org/p/167892/   BWA-mem added XA tag to a read if it is mapped to multiple places. some people also use  sam ...
written 2.3 years ago by tangming2005150
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... I actually used bwa mem to map to get the bam files, so bwa mem is keeping the multi-mapped reads I guess.  You mentioned that `get.reads` only read in the primary alignments? but why it is still there?  Maybe I need to remove those reads in bam before feeding into TEQC? Thank you! Tommy ...
written 2.3 years ago by tangming2005150
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reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not seem to be unique
... Hi, I was running QC for my whole exome data (paired-end sequencing) and got this error: > readpairs <- reads2pairs(reads) Error in reads2pairs(reads) : read pair IDs do not seem to be unique sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: ...
teqc written 2.3 years ago by tangming2005150
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... using 2.3.22 gave me this   > LUSC_rna_data <- GDCprepare(query_rna_LUSC.hg38) |========================================================================================================| 100%    1 MB |============================================================================================ ...
written 2.6 years ago by tangming2005150

Latest awards to tangming2005

Popular Question 10 months ago, created a question with more than 1,000 views. For TxDb.Hsapiens.UCSC.hg19.knownGene misannotation of a gene
Great Question 11 months ago, created a question with more than 5,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 18 months ago, created a question with more than 1,000 views. For IdeogramTrack from Gviz with chromosome name "4" rather "chr4"
Great Question 2.5 years ago, created a question with more than 5,000 views. For DESeq2 for ChIP-seq differential peaks
Centurion 2.5 years ago, created 100 posts.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Gviz GeneRegionTrack draw only one gene in the range
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to bin a GRanges to small bins
Popular Question 2.5 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Supporter 3.6 years ago, voted at least 25 times.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 3.6 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene

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