[mira_talk] Re: Illumina/Solexa sequence coverage.
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 13 Sep 2011 17:27:29 -0400
On 2011-09-13, at 2:21 PM, Bastien Chevreux wrote:
> On Sep 13, 2011, at 18:53 , John Nash wrote:
<snip>
>> b. 30 Sanger reads - these are PCR reads to gap-close the 454 data, from the
>> days when I only had 454 data. Converted to CAF format via
>> phred/phrap/crossmatch to ace format, and then via tg_index to a gap5_db,
>> then gap5 to CAF format. (Tell me there's a faster way!!!).
>
> Ummm ... there is a faster way:
>
> convert_project -f fasta -t CAF input.fasta output
>
> (and it reads qualities from .fasta.qual files if present). In case your
> Sanger did not have clippings (like, e.g., you trimmed the .ab1 beforehand),
> then that's what I'd have used.
>
>> In both experiments, these appear to have ended up in the debris (???)
>
> Hmmm ... question would be: why?
I really do not know. These are genuine PCR-generated reads assembled back in.
Can I re-add them back to an assembly (after first searching to make sure that
they are not hidden in a contig somewhere)?
>
>> PS. I have one question. Can I use the resulting assembly to map against a
>> related genome to use synteny to cover gaps. I know how to do it with a 454
>> assembly but not a hybrid one.
>
> I didn't quite get that question ... what do you want to do?
I guess that I am asking what the command line parameters are to take a CAF
file from a hybrid assembly and then use it as input for a mapping assembly
against a reference genome. Or should I dump the contigs as fastq files and
use those.
I didnt want to do a mapping assembly right from the start as I the genomes are
not *that* closely related. However they are related enough that I'm curious.
John
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