User: tangming2005

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tangming200570
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Posts by tangming2005

<prev • 103 results • page 1 of 11 • next >
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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 11 days 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 12 days 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 12 days 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 19 days 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 4 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 4 months ago by tangming200570
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... installing from github gave me this error. thanks for looking into it > devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master Installin ...
written 4 months ago by tangming200570
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... Now it is randomly use genome annotations... it is human data set, but using elephant genes...   > LUAD_rna_data <- GDCprepare(query_rna_LUAD.hg38) |================================================================================| 100%    1 MB                 |  33% |======================= ...
written 4 months ago by tangming200570
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... thanks, there is another error showed up.   > LUAD_rna_data <- GDCprepare(query_rna_LUAD.hg38) |================================================================================| 100%    1 MB                 |  18% |============================================================================ ...
written 4 months ago by tangming200570
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... Thank you very much for doing it. @tiagochst  how about update `TCGAbiolinks` to use mirrors?   ...
written 4 months ago by tangming200570

Latest awards to tangming2005

Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 16 months ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Supporter 16 months ago, voted at least 25 times.

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