User: Dylan Wang

gravatar for Dylan Wang
Dylan Wang40
Reputation:
40
Status:
New User
Location:
Harbin
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
9 months, 1 week ago
Email:
d************@gmail.com

Posts by Dylan Wang

<prev • 13 results • page 1 of 2 • next >
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Comment: C: On identifying differentially expressed genes using RNA-Seq (fpkm) data.
... Thank you for your help! I will try to obtain DE genes using raw counts. ...
written 4 weeks ago by Dylan Wang40
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Comment: C: On identifying differentially expressed genes using RNA-Seq (fpkm) data.
... I downloaded the FPKM data from GEO database. They just provided the FPKM data matrix. For raw count data, they provided SRA format sequencing data. However, I am in urgent need of data analysis, so I would like to ask if there is any differentially expressed gene analysis method for FPKM. ...
written 4 weeks ago by Dylan Wang40
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On identifying differentially expressed genes using RNA-Seq (fpkm) data.
... I just have FPKM RNA-seq gene expression data, I would like to ask which software or R-package can use fpkm data to identify differentially expressed genes. ...
gene rna-seq written 4 weeks ago by Dylan Wang40
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Comment: C: About TCGA breast cancer HER2 status
... Thank you! I got it. ...
written 4 weeks ago by Dylan Wang40
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About TCGA breast cancer HER2 status
... I have already downloaded the TCGA-BRCA clinical data. I want to divide the tumor sample using HER2 status. But I do not know which item represents the HER2 status? There are a lot of items (contain "HER2" keyword) such as: lab_proc_her2_neu_immunohistochemistry_receptor_status lab_procedure_her2_ ...
rna-seq written 7 weeks ago by Dylan Wang40
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Comment: C: RSEM: The reference contains no transcripts!
... Thank you for your answer! I downloaded some SRA data from NCBI. I read its introduction: Data processing Basecalls performed using bcl2fastq (v2-2.19). Reads were aligned to hg19 reference using STAR (v2.5.2). Transcripts were quantified using RSEM (v1.2.30) and the GRCh37.68 gtf annot ...
written 7 months ago by Dylan Wang40
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RSEM: The reference contains no transcripts!
... I want to use RSEM tool to finish my job. However, I got some question. Here is the code: rsem-prepare-reference --gtf /home/dwang/Data/GRCh/Homo_sapiens.GRCh37.68.gtf --star -p 2 ~/Data/UCSC/hg19.fa /Data/Results There are some errors. I do not know why. Warning: 197611 transcripts are f ...
alignment rna-seq sequencing written 7 months ago by Dylan Wang40 • updated 7 months ago by WouterDeCoster40k
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Convert NCBI SRA data to gene expression data
... I have downloaded some SRA data from NCBI(GEO)? I converted SRA data into fastq format. I want to know how to convert fastq format to Gene Expression Matrix using STAR, RSEM? ...
genome ncbi alignment rna-seq written 7 months ago by Dylan Wang40
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Comment: C: About TCGA CNV data preprocessing
... I think the Error code means there is no element in "sample.tmp". And which() will return nothing. ...
written 8 months ago by Dylan Wang40
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Comment: C: About TCGA CNV data preprocessing
... I have downloaded the masked CNV data filtered germline variation as input data and get the average of all probes per gene. If I just want to use CNV data for cluster analysis, is this right? Thank you for your sharing. Now I know the difference between variation and alteration. Thanks again! ...
written 9 months ago by Dylan Wang40

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Popular Question 27 days ago, created a question with more than 1,000 views. For About TCGA CNV data preprocessing

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