[mira_talk] Re: Paired-end counts
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 1 Oct 2015 16:28:18 -0400 (EDT)
On October 1, 2015 at 12:53 PM "Bridges, Dale" <DBRIDGES@xxxxxxxxxxx> wrote:
[...]
1. I would like to know if the singlets are included in the
Mira_reads_Assembled count (I am assuming they are not).
If singlets are written out to the normal results, they should be counted. Then
again maybe not, because they are not really 'assembled', are they? To be honest
I am not sure what my last line of thought regarding this was.
Maybe that is also the reason that the tracking of reads assembled may have a
bug somewhere, I need to check back on that when time permits.
2. To find out the % reads assembled is this:
[...]
How about making it easier then?
Total reads in contigs: TRC='wc -l *_info_contigreads.txt' - 3
Reads in debris: DEB='wc -l *_info_debrislist.txt'
Reads assembled= 100 /(TRC+DEB) * TRC
B.
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