User: Dylan

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Dylan30
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4 months, 1 week ago
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Posts by Dylan

<prev • 8 results • page 1 of 1 • next >
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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 9 weeks ago by Dylan30
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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 9 weeks ago by Dylan30 • updated 9 weeks ago by WouterDeCoster36k
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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 9 weeks ago by Dylan30
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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 Dylan30
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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 Dylan30
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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 Dylan30
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About TCGA CNV data preprocessing
... 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 ...
snp cnv written 4 months ago by Dylan30 • updated 4 months ago by Kevin Blighe37k
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About TCGA CNV probes
... 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- ...
snp cnv written 4 months ago by Dylan30 • updated 4 months ago by Pin.Bioinf230

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