[mira_talk] Re: where are the singlets ?
- From: Isabelle Lesur <isabelle.lesur.kupin@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Mar 2012 17:34:20 +0100
Hello (again),
I just find out that my debrislist.txt file contains a list of 50 281
contigs...it looks like I have no singlets and many debri...
Isn't that strange?
Isabelle
2012/3/22 Isabelle Lesur <isabelle.lesur.kupin@xxxxxxxxx>
> Hello!
>
> I did use MIRA to perform an assembly consisting of 84086 sanger reads
> with quality.
> At the end of the process, MIRA indicates that 33 805 reads have been
> assembled into 14 101 contigs.
>
> The contigreadlist.txt file indeed contains 33 805 lines, each line
> corresponds to one read associated with one contig of the assembly.
> I thaught the singlets would be among these 14 101 contigs but all the
> contigs in the contigreadlist.txt contain at least 2 reads.
> Does this mean that all the singlets in the assembly were in fact bad
> quality reads that were considered as debri?
> Is there a specific file containg singlets, separated from the result file
> containg contigs?
>
> From what I red in the MIRA doc, the singlets should be in the result file
> with other contigs containing more than one read.
>
> "However, not all reads can be placed in an assembly. This can have
> several reasons and these reads may end up at two different places in the
> result files: either in the *debris* file, then just as a name entry, or
> as singlet (a "contig" with just one read) in the regular results."
>
> Does anybody can help me?
>
> Thanks,
> Isabelle
>
>
Other related posts:
