[mira_talk] Re: 5' trimming of partial adapters
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 19 Jul 2011 18:10:41 -0400
My colleague, Shaun Tyler (also on this list), tells me that with 454
sequencing, there can be concatenation of the end adaptors to make dimers. In
my hands, the second mer is often missing a base or two, and it's not removed
by the primary clipping. sff_extract usually screams at me when that happens,
and so I re-invoke it with " --min_left_clip=16" or somesuch.
John
On 2011-07-19, at 6:00 PM, Robert Bruccoleri wrote:
> In some of the genome assembly projects that I'm working on, I see an uneven
> GC content at the beginning (first 10 bases) of my reads. Since the library
> preparation is expected to be unbiased, uneven GC content suggests that there
> is a contaminant sequence at the beginning of some of my reads.
>
> Let's assume for the sake of argument that the contaminant sequence is a
> short subsequence of an adapter, but it's too short to identify by sequence
> similarity. Does anyone have any ideas about how to handle the problem
> besides trimming the 5' end? Does the option
> -CL:possible_vector_leftover_clip handle this type of problem?
>
> Thanks. --Bob
>
> <bruc.vcf>
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