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.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
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