Read TCGA BAM files into TEtranscripts tool (python) without downloading them?

Question

[Gema Sanz]

Hi,

I wonder if there is any way to read TCGA bam files into linux console to analyze them without need of downloading them. For example, I want to use TEtranscripts from TEToolkit to analyze quite large amoung of TCGA samples but I'm not sure if I could skip the downloading step due to the space requirements.

Any help is very much appreciated.

Gema

[ATpoint]

This tool does not seem to have any integration with the TCGA portal, so I do not see how you would do that. Still, RNA-seq files are not that big, probably a few tens of GBs only, so in the worst case save them on an external disk and then proceed. External drives are really cheap these days even with mutliple TBs of storage capacity. Alternatively, think about a cloud-based solution with e.g. AWS given you do not have access to a HPC at your institution. The latter I would check first.