User: ren.yingxue

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Posts by ren.yingxue

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Comment: C: TCGA raw counts DexSeq
... Hi! I wonder if you were able to turn your raw exon count file into something you can use with DEXSeq? I also have a project with TCGA raw exon counts and don't know how to make it work with DEXSeq. Any suggestions you can give is much appreciated! ...
written 19 months ago by ren.yingxue0
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Comment: C: how to use DEXSeq with raw exon count matrix from TCGA
... thank you for the comments. I cannot use dexseq_count.py because I don't have the BAM files for the ~890 samples. I only have a matrix of raw exon counts downloaded from TCGA. ...
written 19 months ago by ren.yingxue0
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how to use DEXSeq with raw exon count matrix downloaded from TCGA
... Hi, I want to use DEXSeq to identify differential exon usage between ~800 cancer vs 90 normal samples from TCGA. I have a matrix of raw exon counts downloaded from TCGA in the format below: Exon TCGA-66-2742-01A TCGA-L4-A4E5-01A TCGA-86-8671-01A TCGA-77-8008-01A ...
dexseq R exon rna-seq written 19 months ago by ren.yingxue0 • updated 18 months ago by Biostar ♦♦ 20
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calculating LD-tools to calculate D' in DNA sequencing data with unphrased genotype
... Hi, I have a VCF file with a list of ~300 SNPs of interest from exome sequencing. I would like to calculate both D' and r2 for each pairwise comparison using my own sequencing data (as opposed to using HAPMAP/1000G). However, the genotypes in the VCF file are unphased. I have discovered that both VC ...
snp written 2.4 years ago by ren.yingxue0
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trouble downloading annotation result from SG-ADVISER-.txt file does not exist
... Dear all, I uploaded a CNV file to SG-ADVISER to perform annotation (https://genomics.scripps.edu/ADVISER). After uploading the file, I received an email from SG-ADVISER that my annotation is ready and can be downloaded from their website. The download page shows that the file has been annotated an ...
annotation sg-adviser cnv written 3.0 years ago by ren.yingxue0 • updated 24 months ago by sashalippmanbiogps0

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