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Are raw RNA-seq data available for samples of TCGA-LUAD (TCGA data set) ?
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18 days ago
qwzhang0601 ▴ 70

We have applied for the Raw data of TCGA from dbGAP, but we can only find BAM files for aligned reads. We are interested in analysis of repeat elements which usually cannot be mapped to the genome uniquely. So we would need the raw RNA-seq data and map the reads by ourselves. Does anyone have experience to download raw RNA-seq data of TCGA samples from GDC?

Thanks

TCGA RNAseq • 169 views
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You said you had access to GDC (Download raw RNA-seq data from TCGA ) so have you looked around to see if sequence files are available? You should also be able to email GDC help desk and ask: support at nci-gdc.datacommons.io

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Thank you very much. Have contacted with GDC help desk.

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12 days ago
Zhenyu Zhang ▴ 350

To close the loop, you can either download GDC BAMs and convert back to FASTQ, or download FASTQ directly from GDC legacy archive.

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