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
229 stars 30 forks source link

TEcount on multple BAMs #132

Closed cottrellka closed 1 year ago

cottrellka commented 1 year ago

My experiment involves a more complicated design than treatment and control, so running TEtranscripts isn't the best option. I would prefer to get a count file for each BAM, or ideally one file with all of the counts, and then perform the DESeq2 analysis separately so I have more control over the analysis design. Does TEcount support multiple BAM files, or do you have a suggested work around? Thanks.

olivertam commented 1 year ago

Hi,

Thank you for your interest in the software, and sorry for the slow response. We would recommend using TEcount for each BAM, and then combine the output (count files) into a single file, and then perform DESeq2 independently.

Thanks.