search

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
206 stars 29 forks source link

Count output for paired end reads #84

Closed emattei closed 3 years ago

emattei commented 3 years ago

Hi, If I run TEtranscripts with a bam containing paired-end reads the '.cntTable' will report reads or fragments?

Thank you

olivertam commented 3 years ago

Hi,

Thank you for your interest in the software. The count table will report fragment counts when working with paired-end data.

Thanks.

emattei commented 3 years ago

Perfect, thank you vey much for the clarification!