Hi Bastien,
Thank you very much for your reply.
Yes, those reads are identical.
Also I use "-HS:ldn=no", so I expect it is not because of normalisation.
I just checked, actually those reads do not occur in contigs. What is this
mean?
If I use "-OUT:sssip=no", those reads will be in debrislist with flag
"UNSAVED_SINGLETS ".
I would very much appreciate your help.
Best regards, Lyu
----- Original Message -----
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Date: 2016/9/1, Thu 10:53
Subject: [mira_talk] Re: Same singlets,
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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