Hi Biostars,
I used the featureCounts function from the Rsubread package in order to count reads. The first time I used my 'regular' bam files. The second time I used Picard Tools to mark duplicates in each bam file and used this data as substrate. I am getting the same number of counts in both cases using featureCounts. I was wondering if it is possible to tell featureCounts to exclude duplicates from the counting. Is there an option doing it within Rsubread or do I have to actually remove (as opposed to mark) the duplicate reads?
Thanks
Sometimes in reserach "in days" can turn into weeks, months etc.
Do you know of any official release date for 1.4.5?
Sorry that it was delayed for weeks. The 1.4.5 version of subread (inc. featureCounts) was released yesterday on sf.net.
http://sourceforge.net/projects/subread/