[Temima]

Here's the script, Hope it works.
Just to clarify - I was given the 454 data in fasta format, not SFF.

I'd be interested in hearing how things go for you.

[ganga.jeena]

thanks

thanks 4 the script

[ganga.jeena]

>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?

[Temima]

the problem is with the lower case bases. change all bases to capital letters and then try

[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 could this error mean?
I have 500 GB RAM working system...
the READMAP file is 23 GB and Sequence file 9.6 GB

dont get it

[ganga.jeena]

Dear Temima,
Whts the configuration of ur machine?

[Temima]

How many reads are you giving velvet?
The program itself is limited in the number of reads it can handle, even if your machine isn't.
I'm working on the cluster located on our solid 3 machine. not optimal, but an ok temporary solution.

[ioannis]

Dear Temima,

I wonder whether you have found a solution with the denovoadp problem. I am running into the same problem "reads match to negative position".

Best,
Ioannis

[Temima]

afraid not

SOLiD support suggested a new tool called Cortex which is supposed to be uploaded to sourceforge soon. So far, it's not there.

http://sourceforge.net/projects/cortexassembler/files/

[sklages]

They put a source tarball into SVN,
http://cortexassembler.svn.sourceforge.net/