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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Whether TEtranscripts can calculate TE expression level of transcripts (NOT Gene)? #13

Closed xflicsu closed 5 years ago

xflicsu commented 7 years ago

As the title asked. Whether TEtranscripts can calculate TE expression level of transcripts (NOT Gene)?

yingjin07 commented 7 years ago

The current version only provides TE expression on element (subfamily) level not each insertions (transcripts).

xflicsu commented 7 years ago

Is it reasonable to replace gene_id name to transcript_id name in rmsk_TE.gtf file? And then count the reads located in each insertions (transcripts). As the gtf file shows us that one element (subfamily) containing several loci. It is not clear to get the expression of one specific insertions.

yingjin07 commented 7 years ago

The reason that we don't output transcript level abundance is that we don't think that the current methods and the technology can give reliable/accurate estimation.