SRR sample ID
Does anyone know how I can convert SRR sample Id to TCGA sample barcode ?
tcgabiolinks
rna-seq
sampleid
r
cancer
programming
• 2,201 views
•
link
updated
by
Hamid Ghaedi
•
written
by
mahsa •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
cBioportal: Mutations in the database don't appear in the portal
written by Camilo Andres •Hi! I am working with the invasive breast cancer database from the pancancer project of TCGA downloaded through cbioportal (https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018). Working with it in R, …
-
KEGG enrichment dotplot
written by mahsa •Hello friends. I'm trying to visualize a dotplot using enrichplot package in R for KEGG and GO object created by enrichKEGG and enrichGO function of …
-
Getting sample IDs from dbGaP SRR?
written by vctrm67 •Does anyone know how to get the actual sample IDs from downloaded and extracted SRA files? Right now they are in the form "SRR..._dbGaP" but …
-
Samples with same TCGA barcode in TCGA data
written by VasuHi, I had downloaded TCGA RNA-seq data using tcgabiolinks package. In the data I see that there few samples with same barcode. Which sample should …
-
CNV from TCGA data
written by emiliakozlowskaa •Hi, I need to analyze copy number variation data from TCGA. I have downloaded all data but several things are not clear with the data. …
-
where can I find the "code table report" for TCGA barcode?
written by haohanwI need to figure out which cancer the data is corresponding to from barcode, and according to the information [here][1], the second label on the …
-
TCGA UUID change back to TCGAbarcode
written by Peter ChungI downloaded the RNA Seq data TCGA Legacy Archive, all the rsem.gene.normalized_results is UUID, how can I know the TCGA barcode back because I can't …
-
how to find sample type information from TCGA?
written by aichen •After download batches of gene expression files from TCGA [gdc][1] (about 600 hundreds files), each file contains only one sample. I wanna know which file …
-
Batch ID in TCGA database
written by Na SedHi, I have downloaded some data from TCGA and I need to remove their batch effects using 'combat' algorithm from sva package, but 'combat' function …
-
TCGA barcode (Genome-wide SNP6 dataset)
written by imagineydHello everyone, I have one question about TCGA barcode. I know the logic of TCGA barcode (from [here][1]). But I find strange TCGA barcodes from …
By SRR you mean SRA run file ID? Can you post some of the Ids here?
yes. for example :
These IDs come from GTEx through SRA. So they are not part of TCGA and you can not map these SRR ids to the TCGA barcode!