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

TEcount processes multiple bam files at the same time #104

Closed shijiu001 closed 2 years ago

shijiu001 commented 2 years ago

Hello, thank you for providing such a useful TE analysis tool. I would like to ask if TEcount can only handle one bam file at a time, or can it handle multiple bam files at the same time as TEtranscripts does? Maybe output a table containing the representation of each TE in each sample.

olivertam commented 2 years ago

Hi,

Thank you for your interest in the software. The rationale behind TEcount was to be able to parallelize the processing of BAM files, so you can run multiple TEcount at the same time. As such, it only handles one BAM at a time. What we do to create the table that you describe (and one that TEtranscripts generates), is just to combine the TEcount output tables using Unix join (or other similar approaches), using the feature name as the key.

Thanks.