Hi, our group would like to switch to featureCounts <http://green-l-bio.ethz.ch:8090/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2> but we are using only GFF from NCBI. It looks like featureCounts <http://green-l-bio.ethz.ch:8090/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2> 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 5186527 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> www.ap.ethz.ch