Question: Where can I find the analysis ID to Firehose TCGA RNA-Seq samples
0
gravatar for -_-
2.5 years ago by
-_-830
Canada
-_-830 wrote:

I have been able to download RNA-Seq expression levels from Firehose, and it looks like

python>  import fbget
python>  print fbget.mrnaseq("egfr", cohort="ucs")
tcga_participant_barcode    gene    expression_log2 z-score cohort  sample_type protocol    geneID
TCGA-QN-A5NN    EGFR    7.06162500905   -0.59899352506  UCS TP  RSEM    1956
TCGA-QM-A5NM    EGFR    8.16734387649   -0.298443593752 UCS TP  RSEM    1956
TCGA-NG-A4VW    EGFR    8.93092623547   0.0932667888031 UCS TP  RSEM    1956

However, I thought the sample identification is not specific enough because each (tcga_participant_barcode, cohort, sample_type) forms an ID for each sample. E.g. what if a participant have multiple EGFR TP samples? I learned from my metadata downloaded from CGHub previously that it's possible for the same patient to have multiple TP samples in the same cohort, and they are identified the a unique analysis ID that looks like 8b846dc9-2a7b-4145-aa7e-c9b5af8beeda. Where are the additional samples in Firebrowse?

firebrowse rna-seq tcga firehose • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by -_-830

I don't see the use of adding "urgent" to your post, you won't get a higher priority. Everyone here is a volunteer and will reply whenever that suits the best.

ADD REPLYlink written 2.5 years ago by WouterDeCoster40k

Thanks. I removed it.

ADD REPLYlink written 2.5 years ago by -_-830
0
gravatar for -_-
2.5 years ago by
-_-830
Canada
-_-830 wrote:

I ended up bulk downloading all RSEM gene normalized data from firehose with firehose_get. It seems to work, and the download data contains longer barcode, specific enough for my usage.

/firehose_get  -o RSEM_genes_normalized__data.Level_3 stddata latest
ADD COMMENTlink written 2.5 years ago by -_-830

Still, the TCGA barcode is not specific enough to can correspond to multiple analysis IDs. :(

ADD REPLYlink written 2.5 years ago by -_-830
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