# RNAseq transcript annotation

**URL:** <https://forum.depmap.org/t/rnaseq-transcript-annotation/2235>\
**Category:** Q&A\
**Created:** [January 26, 2023, 4:50am UTC](https://forum.depmap.org/t/rnaseq-transcript-annotation/2235 "2023-01-26T04:50:10Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Yanjing\_Liu](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yanjing_liu/32/754_2.png) [@Yanjing\_Liu](https://forum.depmap.org/u/Yanjing_Liu)\
**Post date:** [January 26, 2023, 4:50am UTC](https://forum.depmap.org/t/rnaseq-transcript-annotation/2235/1 "2023-01-26T04:50:10Z")

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Hi, I’d like to check the expression level of genes using the RNAseq data from CCLE. However, I only see the gene ID in the file without the corresponding transcript ID, making it difficult to understand which isoform has been used for the analysis. May I know the criteria of picking transcript for this analysis? Many thanks!

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [February 1, 2023, 8:45pm UTC](https://forum.depmap.org/t/rnaseq-transcript-annotation/2235/2 "2023-02-01T20:45:23Z")

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Hi,

Thanks for reaching out!

I am assuming you are using OmicsExpressionProteinCodingGenesTPMLogp1.csv in the “primary files” section in the download page. It contains RSEM’s gene-level abundance estimates which are essentially a summary of all isoforms for each gene. If you want to see transcript-level abundance estimates, you should be able to download OmicsExpressionTranscriptsExpectedCountProfile.csv in the “all files” section which contains expected counts on the transcript level. Hope this helps!

Simone

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**Author:** ![Yanjing\_Liu](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yanjing_liu/32/754_2.png) [@Yanjing\_Liu](https://forum.depmap.org/u/Yanjing_Liu)\
**Post date:** [June 14, 2023, 5:36pm UTC](https://forum.depmap.org/t/rnaseq-transcript-annotation/2235/3 "2023-06-14T17:36:43Z")

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Hi, thank you so much for the clarification! I indeed found the “OmicsExpressionTranscriptsExpectedCountProfile.csv” to get transcript level RNA-seq value. Could I double check what are the values in this file? I would assume they are the TPM value calculated from RSEM tool, is it correct? Thanks!

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [June 14, 2023, 7:04pm UTC](https://forum.depmap.org/t/rnaseq-transcript-annotation/2235/4 "2023-06-14T19:04:48Z")

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Hi,

“OmicsExpressionTranscriptsExpectedCountProfile.csv” contains expected counts, not TPM. If you are looking for transcript-level TPM specifically, you might want to check out OmicsExpressionTranscriptsTPMLogp1Profile.csv.

Best,  
Simone