Hi,
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 |
| 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