Question: Remove duplicates in featurecounts
0
gravatar for lkmklsmn
4.8 years ago by
lkmklsmn870
United States
lkmklsmn870 wrote:

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 

ADD COMMENTlink modified 4.8 years ago by dbpzdbpz90 • written 4.8 years ago by lkmklsmn870
2
gravatar for dbpzdbpz
4.8 years ago by
dbpzdbpz90
Australia
dbpzdbpz90 wrote:

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.

ADD COMMENTlink written 4.8 years ago by dbpzdbpz90

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

Do you know of any official release date for 1.4.5?

ADD REPLYlink written 4.8 years ago by lkmklsmn870

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/

ADD REPLYlink written 4.8 years ago by dbpzdbpz90
0
gravatar for Chris Fields
4.8 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

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

ADD COMMENTlink written 4.8 years ago by Chris Fields2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1257 users visited in the last hour