ask about solid read assembly

[bah]

Hi

could you please tell me if CURTAIN could assembly colourspace reads
to contigs(basespace)?

thanks

[Matthias]

Hi,

I haven't tried to run colourspace (NOT hybrid) assemblies with
Curtain, but in theory it should be possible. In oder to get curtain
running, you need
1) input contigs (as usual in sequence space)
2) BAM files, where the colourspace reads are mapped against the
contigs
3) modify the CurtainConfig.properties to point to a velvet version
compiled for colourspace (see <path-to-curtain>/classes/uk/ac/ebi/
curtain/configuration/)

I'm currently working to release a new version of Curtain - if you
would like to give it a try, I could send you a snapshot version.

Best,
Matthias

[bah]

ok,thanks alot.

I also wonder if the contigs must be input as reference. Could i do
denove assembly without contigs?

Please sent me a snapshot version.

Email:
hengx...@agresearch.oo.nz

Tnanks

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[bah]

hi

Thanks your reply!

If should be possible, the double-encode sequence reads would be used
in velvet(velvetg_de,velveth_de). Is it thus?

I want to use BOWTIE to map solid reads agaist contigs to produce SAM
file.

It seem like inconsistency between double-encode reads in velvet and
colorspace reads in SAM file in pipeline,isn't it?

Thanks!

On Mar 3, 10:01 pm, Matthias <mhaimel....@googlemail.com> wrote:

[Matthias Haimel]

Down to the following post from the velvet-users email list, double-encode sequence
reads should work with velveth_de and velvetg_de:
http://listserver.ebi.ac.uk/pipermail/velvet-users/2009-June/000414.html

I used BOWTIE for read mapping before with sequence reads, not with colorspace reads,
but looking at the manual it should work.

Regarding the inconsistency - could you send me an example what you mean?

Hope this helps,
Matthias

[bah]

Thanks ,I will have a try.

On Mar 11, 12:20 am, Matthias Haimel <mhaimel....@googlemail.com>
wrote:

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