In TCGA: R1 and R2 files are missing in fastq.gz

Question

[archana.bioinfo87]

Hi,

I downloaded some RNA-seq data from TCGA. After doing untar I realized the R1 and R2 fastq files are not there.

For example UNCID_2210756.2c113ebf-70de-4752-81de-a873f4f3db64.110324_UNC6-RDR300211_00088_FC_7090HAAXX_4.tar

To untar this I used command "tar -xvf UNCI*.tar" And got a single fastq file 110324_UNC6-RDR300211_00088_FC_7090HAAXX_4.fastq

Any one please suggest what is happening here.

Any help is much appreciated.

Thanks

[Kevin Blighe]

The TCGA data has been 'sprayed' all over the web. From which source did you download, and how?

[archana.bioinfo87]

I downloaded from this link https://portal.gdc.cancer.gov/legacy-archive/search/f

As, I have access for controlled data sets.

Answer 1

[Kevin Blighe]

It is likely single-end data. Can you paste some of the reads and their headers from the fastq file?

[archana.bioinfo87]

Yes, thanks for this hint. I solved my problem.