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Remove duplicates in featurecounts

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

featurecounts picard rna-seq rsubread
• 5,686 views • link
updated by Ram Ram • written by lkmklsmn lkmklsmn

2 answers

The new version of subread (1.4.5) will provide a function to ignore reads or fragments that have the 0x400 flag (the duplicate read flag). This version should be released in days.

• 3 views • link
written by dbpzdbpz dbpzdbpz

Sometimes in reserach "in days" can turn into weeks, months etc.

Do you know of any official release date for 1.4.5?

• 0 views • link
written by lkmklsmn lkmklsmn

It doesn't look as if this is supported, though technically it shouldn't be hard to add (they already parse read bit flags and attributes). Maybe ask the authors? Mailing list is here:

https://groups.google.com/forum/#!forum/subread

• 3 views • link
updated by Ram Ram • written by Chris Fields Chris Fields

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