Jin

Could it be that you haven't used enough memory?

Please try our docker version at: https://hub.docker.com/r/jinwashu/integrate

Hi Arnold, Please refer to https://github.com/ChrisMaherLab/INTEGRATE-Vis, which contains the detailed commands for generating annotation files, and addtional examples. As for the test case here, becasue the sample BAM was on hg19/GRCh37, you have to stick to the version of the reference. You can just grep chr6 and 19 using the annotation file with 11 columns here to make the test case work. Thanks, Jin

Hi, To make the test case work, the annot file need to be taylored. Pease see attached. Thanks, JIn

Have you run "mkbwt"?

Problem with annotation file

Hi Mauro, You can try using the file annot.ensembl.txt at https://sourceforge.net/projects/integrate-fusion/files. There is also a wiki page about creating gene annotation file for INTEGRATE, https://sourceforge.net/p/integrate-fusion/wiki/annotation/. Thanks, Jin

The annotaion file in the test case is too old. Please use the one under the Files...