[mira_talk] Re: Same singlets,

From: Bastien Chevreux <bach@xxxxxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Date: Wed, 31 Aug 2016 22:53:21 -0400

On 30 Aug 2016, at 20:23 , wakamoto5959@xxxxxxxxxxx wrote:

After an assembly, if I check singlets in out.unpadded.fasta file, many of
those singlet reads are exactly same sequence.
So I am wondering why this is happening.

I’m terribly sorry, atm I do not have the time to look at your data.

“Same sequence” is a bit unclear:
- are the reads identical? This could point at repeats so nasty that MIRA
masked them out / made a read normalisation.
- do the singlets contain sequence identical to contigs? This could point at
problems with the paired end distance or nasty repeats.

What you can do: do NOT use -OUT:sssip and then look at the debris file what
reason is mentioned there.

B.

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References:
- [mira_talk] Same singlets,
  - From: wakamoto5959

[mira_talk] Re: Same singlets,

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