Decompressing data from EGA

[JJZ]

Hi everyone,
Has anyone encountered decompressing problems with dataset from European Genome-Phenome Arichives (EGA) before? I downloaded some RNAseq data. The files all have the .fastq.gz suffix. But gunzip -d could not decompress any of the files, saying they are not in gzip format. FASTQC also didn't accept it, citing the same problem. It looks like that for each sample there are two .fastq.gz files, so I merged two files using cat. But it didn't help either.

I am still very new to this. Am I doing it wrong? Should I have used different commands to decompress it ?

Thanks in advance.

[dpryan]

Do you actually have access to the dataset? They're encrypted afterall.

[JJZ]

Yes I do. I applied and was granted access and I decrypted the files using their client software

[dpryan]

My only guess would be that you somehow received a corrupted file. The first thing to do would be to redownload and see if that solves the problem (just do one file to save time). If that doesn't solve the problem, I'd recommend contacting the EGA help-desk.

[JJZ]

Thanks for the suggestion. Seems that the majority of the files are corrupted. I re-downloaded another one and it can be decompressed just fine.