You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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:
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
The text was updated successfully, but these errors were encountered:
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:
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
The text was updated successfully, but these errors were encountered: