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Forum: 454 Pyrosequencing 12-04-2011, 03:22 AM
Replies: 6
Views: 3,789
Posted By ganga.jeena
Dear SABC, I need a refernce paramter filtering...

Dear SABC,
I need a refernce paramter filtering for 454 Data.
Can you mail me a copy of filterTemplate.xml pre and post changes .
I will be very thankful for the same.
Regards,
Ganga Jeena
Forum: Bioinformatics 05-25-2011, 05:37 AM
Replies: 22
Views: 11,312
Posted By ganga.jeena
Is there any limitation to the input sequence...

Is there any limitation to the input sequence size into CAP3.
I want to combine assemblies from 454 and illumina using CAP3. However I find most of the contigs in singleton_file generated by cap3....
Forum: Bioinformatics 02-16-2011, 08:58 PM
Replies: 0
Views: 2,145
Posted By ganga.jeena
Unhappy Regarding assemblers

Dear All,
I got a lot of illumina data and AbySS gives me odd errors and fail to complete with test data
For my solexa data it just gives errors taht it cannot read my files.
I have downloaded...
Forum: Bioinformatics 02-14-2011, 07:10 PM
Replies: 1
Views: 1,601
Posted By ganga.jeena
Regarding gsAssembler and different results on same dataset

Could someone please explain why does the result differs everytime with the same set of data in gsAssembler ? :confused:
Forum: Bioinformatics 01-28-2011, 01:26 AM
Replies: 1
Views: 1,838
Posted By ganga.jeena
Regarding Solexa data

What exactly does the following mean:

63_k/nohup.out

Output 285695310 out of 495475004 (57.7)% reads in gaps :confused:
352330547 out of 495475004 (71.1)% reads mapped to contigs
...
Forum: Bioinformatics 01-08-2011, 12:26 AM
Replies: 22
Views: 11,312
Posted By ganga.jeena
Happy new year

This is too late...
but just want to know if u tried PCAP ?
Forum: Bioinformatics 01-07-2011, 09:24 PM
Replies: 0
Views: 1,235
Posted By ganga.jeena
Regarding CONSORT

Dear All,
A Very Happy New Year !!:)
If someone has used or is having CONSORT could you please provide me with it.
I want to use it for scaffolding 454 ata using SOLID data.
Regards,
Ganga Jeena
Forum: Bioinformatics 12-31-2010, 12:25 AM
Replies: 0
Views: 2,509
Posted By ganga.jeena
Regarding PCAP and CAP3

:)Happy New Year to all !

Has someone used PCAP or CAP3 for their ssembly or scaffolding purpose ?

Plase guide me with the program as to how should i run PCAP for single end data.
I am getting...
Forum: Bioinformatics 12-20-2010, 08:12 PM
Replies: 2
Views: 3,816
Posted By ganga.jeena
Question Regarding paired -end assembly insert-size calculation on newbler2.3

pairedReadStatus
{
numberWithBothMapped = 1157826;
numberWithOneUnmapped = 229595;
numberMultiplyMapped = 715851;
...
Forum: Bioinformatics 12-20-2010, 01:32 AM
Replies: 252
Views: 118,045
Posted By ganga.jeena
congrats

:)
Its grt to hear such an achievement.
Is your paper freely available.
Can you mail me downloadable software copy
Regards,
Ganga Jeena
Forum: Bioinformatics 10-12-2010, 02:57 AM
Replies: 24
Views: 11,087
Posted By ganga.jeena
Dear Temima, Whts the configuration of ur...

Dear Temima,
Whts the configuration of ur machine?
Forum: Bioinformatics 10-12-2010, 02:56 AM
Replies: 24
Views: 11,087
Posted By ganga.jeena
Regaarding velvetg_de

Error:

velvetg: Can't calloc 18446744072095878219 Annotations totalling 18446744009162615736 bytes: Cannot allocate memory
Reading roadmap file /home/data/7_oct/777//Roadmaps

exit


Wht...
Forum: Bioinformatics 10-11-2010, 02:15 AM
Replies: 24
Views: 11,087
Posted By ganga.jeena
>contig00001 length=1782 numreads=47 ...

>contig00001 length=1782 numreads=47
GAAcAAagaG

>contig00001 length=1782 numreads=47
200200202

the output doesnt seem to be correct , can u check it up with the min bases above?
Forum: Bioinformatics 10-11-2010, 01:55 AM
Replies: 24
Views: 11,087
Posted By ganga.jeena
Smile thanks

thanks 4 the script
Forum: Bioinformatics 10-10-2010, 09:05 PM
Replies: 24
Views: 11,087
Posted By ganga.jeena
hello Temima glad to know of the gud news cd...

hello Temima
glad to know of the gud news
cd u forward me the script for 454 to color spce conversion,

i hv been also trying to combine 454 and SOLiD data for assembly hwver my experimental...
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