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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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Obtain the chromosome (start/end) position after running SalmonTE.py quant #42

Closed ferygood closed 4 years ago

ferygood commented 4 years ago

Hello,

Is there a way to know the chromosome position (e.g. chr1 145233 145561) where my reads map to after running SalmonTE.py quant?

Because after running SalmonTE.py quant, I can only view the TPM or count in the EXPR.csv. I want to know which start/end position do the TEs actually map to the reference.

Thank you for your help!

hyunhwan-jeong commented 4 years ago

Hello @ferygood,

The goal of the SalmonTE is to quantify the overall abundance of each TE from a sample, and it doesn't report the position. The reason SalmonTE only quantifying the overall abundance is that RNA-seq has an instinct problem to locate the position because of the mapping ambiguity issue.

Best,

Hyun-Hwan Jeong

ferygood commented 4 years ago

Hello Hyun-Hwan

Thank you for your detailed reply! SalmonTE is really a fast tool to quantify TEs from RNA-seq data and I appreciate your work.

Best, Yao-Chung Chen