Exon-Exon junction counts

Q&A
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1

Hi,

I have seen in the CCLE 2019 article (Next-generation characterization of the Cancer Cell Line Encyclopedia | Nature) exon-exon junction counts were quantified with STAR to obtain the exon inclusion ratios that are available in DepMap’s downloads section (CCLE_RNAseq_ExonUsageRatio_20180929.gct.gz). Would it be possible to have the exon-exon junction read counts table that originated that file?

Thanks very much in advance, best,

Miquel

2

Hi,

Unfortunately we currently do not release junction counts data. However, if you are interested in CCLE 2019 data specifically, we do have raw bam files publicly available for all the cell lines referenced in the paper that you can generate junction counts from.

Thanks,
Simone

3

Hi, thank you for your help. However, starting with bam files I am not sure I will obtain the same output as STAR so I think I will have to align them again.

Best,

Miquel