User: Dylan
Dylan • 30
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- 30
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- New User
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- Google Scholar Page
- Last seen:
- 3 weeks, 2 days ago
- Joined:
- 4 months, 1 week ago
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- d************@gmail.com
Posts by Dylan
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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 9 weeks ago by
Dylan • 30
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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 9 weeks ago by
Dylan • 30
• updated
9 weeks ago by
WouterDeCoster ♦ 36k
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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 9 weeks ago by
Dylan • 30
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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 3 months ago by
Dylan • 30
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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 4 months ago by
Dylan • 30
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Comment:
C: About TCGA CNV data preprocessing
... Hi,
Thanks for your help!
I just downloaded the CMV data from TCGA database and mapped genomic regions to gene symbols using the following code:
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
genes <- getBM(attributes=c("hgnc_symbol","chromosome_name","start_posit ...
written 4 months ago by
Dylan • 30
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... Hello all,
I am looking at the Level 3 CNV files on TCGA. I have a few questions:
I download copy number variance data from TCGA database and mapped genomic regions to gene symbols using this method(https://www.biostars.org/p/311199/#311746). Now i get a matrix that its rows are genes and its colum ...
written 4 months ago by
Dylan • 30
• updated
4 months ago by
Kevin Blighe ♦ 37k
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... Hello all,
I am looking at the Level 3 CNV files on TCGA. I have a few questions:
I have downloaded the CNV data from TCGA. The details are as follows:
GDC_Aliquot Chromosome Start End Num_Probes Segment_Mean Sample
9f3983d5-2f2d-4761-9b4d-4a2ea22ada7b 1 62920 953279 64 -0.2437 TCGA-AR-A0U0-10A- ...
written 4 months ago by
Dylan • 30
• updated
4 months ago by
Pin.Bioinf • 230
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