RNA sequencing bioinformatic analysis (CEL.gz file)

Question

[bioinformatics]

Hi,

I am trying to perform fastqc on data downloaded from NCBI for rna sequencing.

However I have samples that are in CEL.Gz file format e.g. GSM4837048_JX65.CEL.gz

But the tutorial has samples in SRR8668755.fastq.gz file format

Do you know if its still possible for me to perform fastqc for quality control on Mac in terminal using the following commands with CEL.GZ file:

conda activate rnaseq
fastqc GSM4837048_JX65.CEL.gz

I get the following error message: Failed to process GSM4837048_JX65.CEL.gz

Thanks for your help!

Answer 1

[Basti]

.CEL files are from microarray, it is not RNA sequencing, it is impossible to convert to .fastq which are sequence data. You can't use fastqc for that type of data

[bioinformatics]

Ok thanks, could you also advise me on how I might run a microarray gene expression comparison analysis?

[ATpoint]

Read the limma manual, and search previous posts. It is only a matter of effort as array questions have been asked extensively for the last 10-15 years.