Using DCC on TCGA data #106
Description
Hello,
I would like to use DCC on TCGA samples using the bam files available on GDC Data Portal. Unfortunately, fastq files are not avaiable (even with full authorized access to data), the only bam files available are generated using STAR 2 and are:
- Aligned Transcriptome
- Aligned Genomic
- Aligned Chimeric
more details are present here:
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#rna-seq-alignment-command-line-parameters
The data are paired, so perhaps I can use samtools to retrieve the fastq from the bam, however I don't know which of the bam files available is better for that use!
Thanks for any help you can address
Pietro