Question

RNA seq tximport

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tanyabioinfo ▴ 20

@tanyabioinfo-14091

Last seen 5.8 years ago

Hi

I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this.

Regards

Tanya

tximport • 1.0k views

ADD COMMENT • link 7.1 years ago tanyabioinfo ▴ 20

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Hi Michael

Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of variation among the replicates. Can you please help me why this would be happening.

Thanks

Tanya

ADD REPLY • link 7.1 years ago tanyabioinfo ▴ 20

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tximport just collates the TPM, it’s not doing the estimation of TPM

ADD REPLY • link 7.1 years ago Michael Love 43k

score 0 · Answer 1 · 2017-11-02

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Michael Love 43k

@mikelove

Last seen 5 days ago

United States

Yes, txi$abundance is the TPMs estimated by Salmon.

ADD COMMENT • link 7.1 years ago Michael Love 43k