User: Dylan Wang
Dylan Wang • 40
- 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
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... Thank you for your help! I will try to obtain DE genes using raw counts. ...
written 4 weeks ago by
Dylan Wang • 40
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... 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 Wang • 40
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... 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. ...
written 4 weeks ago by
Dylan Wang • 40
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... Thank you! I got it. ...
written 4 weeks ago by
Dylan Wang • 40
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... 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_ ...
written 7 weeks ago by
Dylan Wang • 40
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... 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 Wang • 40
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... 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 ...
written 7 months ago by
Dylan Wang • 40
• updated
7 months ago by
WouterDeCoster ♦ 40k
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... 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? ...
written 7 months ago by
Dylan Wang • 40
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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 Wang • 40
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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 Wang • 40
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For About TCGA CNV data preprocessing
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