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Search: Posts Made By: vani s kulkarni
Forum: Illumina/Solexa 09-09-2009, 07:15 AM
Replies: 3
Views: 4,446
Posted By vani s kulkarni
EDENA assembler

Hi
Am using EDENA assembler for my solexa reads.
and this is the first time am using with default settings but while runing
it came as -Elongations were stopped because of:
...
Forum: De novo discovery 08-28-2009, 02:28 AM
Replies: 1
Views: 30,708
Posted By vani s kulkarni
velvet and SOAPdenovo assembly

hi
I have used the velvet and SOAPdenovo for my solexa reads.
Can any one explain how can I compare cotig from both results?
I have used the same k-mer in both case.

And

I know that people...
Forum: Bioinformatics 08-20-2009, 06:00 AM
Replies: 0
Views: 1,487
Posted By vani s kulkarni
velvet and SOAPdenovo assembly

hi
I have used the velvet and SOAPdenovo for my solexa reads.
Can any one explain how can I compare cotig from both results?
I have used the same k-mer in both case.

And

I know that people...
Forum: Bioinformatics 08-12-2009, 06:12 AM
Replies: 6
Views: 4,497
Posted By vani s kulkarni
SOAPdenovo

Hi

I want to use SOAPdenovo assembler for my solexa short reads.
But am not understanding what is Configuration file and how can I do that? Can any one explain me this Configuration file and ...
Forum: Bioinformatics 07-30-2009, 02:50 AM
Replies: 1
Views: 3,224
Posted By vani s kulkarni
Java for bioinformatics..

hi
Am new to Java programing and am looking for Java program examples which are related to the molecular biology. In on line most of the time it would be a Hello world example or metamathematical...
Forum: Bioinformatics 07-10-2009, 02:00 AM
Replies: 4
Views: 6,225
Posted By vani s kulkarni
velvet- stats.txt file

hi
I am using velvet for my solexa reads(36bp).
Can any one explain the use of stats.file, as it will be having the following information

ID, lgth, out, in, long_cov, ...
Forum: Bioinformatics 07-06-2009, 02:39 AM
Replies: 25
Views: 14,574
Posted By vani s kulkarni
hi Thanks for your informations ,now I can...

hi
Thanks for your informations ,now I can try with different options...
Forum: Bioinformatics 06-10-2009, 12:40 AM
Replies: 25
Views: 14,574
Posted By vani s kulkarni
hi thanks for the link but I want to know...

hi
thanks for the link

but I want to know how this hash length helps in selecting good assembly?
Forum: Bioinformatics 06-10-2009, 12:36 AM
Replies: 25
Views: 14,574
Posted By vani s kulkarni
hi how to select good assembly based on...

hi

how to select good assembly based on hash length and N50 in velvet denovo assembler?
Forum: Bioinformatics 06-08-2009, 04:05 AM
Replies: 25
Views: 14,574
Posted By vani s kulkarni
velvet assembly

hi

Am using 'Velvet' assembly for my short read sequence from solexa.
I want to know about the parameters like hash length (K) and N50 in velvet in detail and in the manual these are not...
Forum: Introductions 06-04-2009, 05:20 AM
Replies: 373
Views: 129,896
Posted By vani s kulkarni
hello everyone, I am vani from Netherlands....

hello everyone,
I am vani from Netherlands. I've just started working with solexa short read sequence for identification of SNPs and I will do further data analysis.....And glad to meet you all...
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