CCLE RNAseq raw counts for all ~1300 lines

Q&A
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1

Hi,

Firstly, this is an amazing resource, thank you!

I could only find the RNA-seq rawcounts for ~1020 cell lines (CCLE). There seems to be normalised expression for > 1300 lines in the latest release (21Q2). Are the raw counts available for these additional 300 cell lines as well?

Thank you for your help!

2

Hi, for the 21Q2 raw counts are you looking at either of these two files in the download page?
CCLE_expression_transcripts_expected_count.csv CCLE_expression_proteincoding_genes_expected_count.csv

3

Is there available raw counts (that is not RSEM or TPM or expected counts) for CCLE?
RSEM and TPM cannot be used with DESeq2 or EdgerR :frowning:

4

Hi @dan3,

Unfortunately we don’t have raw counts available at the moment, but for the CCLE lines you should be able to access the raw bam files publicly available in this terra workspace and generate them yourself.

Thanks!
Simone