our group would like to switch to featureCounts but we are using only GFF from NCBI. It looks like featureCounts provides GFF but out of the box it does not provide a proper count table. The output looks like this:

Status HISAT2 on data 33
Assigned 5186527
Unassigned_Unmapped 518985
Unassigned_MappingQuality 1353602
Unassigned_Chimera 0
Unassigned_FragmentLength 0
Unassigned_Duplicate 0
Unassigned_MultiMapping 0
Unassigned_Secondary 0
Unassigned_Nonjunction 0
Unassigned_NoFeatures 7515020
Unassigned_Overlapping_Length 0
Unassigned_Ambiguity 0

Geneid HISAT2 on data 33


I guess I need some advanced options? Which are different to the default run settings?

Does anyone have a tutorial or example on how to configure the tool correctly with a standard GFF file, or does anyone also use GFF files? Or is there a better tool to use?

Cheers Jochen

ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
jochen.bick@usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch>