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