User: tangming2005

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tangming200570
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Posts by tangming2005

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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 23 days ago by tangming200570
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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 23 days ago by tangming200570
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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 23 days ago by tangming200570
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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 24 days ago by tangming200570 • updated 23 days 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 9 weeks ago by tangming200570
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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 9 weeks ago by tangming200570
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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 9 weeks ago by tangming200570
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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 11 weeks ago by tangming200570
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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 6 months ago by tangming200570
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... yes, that worked if I install psych first. ...
written 6 months ago by tangming200570

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Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 18 months ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
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