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Forum: Bioinformatics 08-18-2015, 06:29 AM
Replies: 6
Views: 2,832
Posted By Ramprasad
Problems in assembling mitochondrial genome

Hi all,

I have assembled a genome (from illumina data) for a non-model species using allpaths and I'm searching for the mitochondria. I have a list of proteins (13 in total) that should be on...
Forum: Bioinformatics 05-22-2015, 05:56 AM
Replies: 4
Views: 3,426
Posted By Ramprasad
Thank you very much GenoMax. Using the...

Thank you very much GenoMax.

Using the latest one did it for me. The program is now running past that stage. Hopefully, it will run to the end.

Cheers,
Ram
Forum: Bioinformatics 05-22-2015, 03:35 AM
Replies: 4
Views: 3,426
Posted By Ramprasad
Thank you very much for your reply GenoMax. ...

Thank you very much for your reply GenoMax.

I did check. But I don't think memory was really a problem here, because I am running this on a server with a terabyte of RAM. And moreover mauve was...
Forum: Bioinformatics 05-22-2015, 02:12 AM
Replies: 4
Views: 3,426
Posted By Ramprasad
Progressive Mauve error

Hi all,

I'm trying to run progressive mauve on three Drosophila genomes with the following command,

/data/programs/mauve_2.4.0/linux-x64/progressiveMauve --output=alignment.xmfa...
Forum: Bioinformatics 11-23-2011, 07:51 PM
Replies: 13
Views: 5,343
Posted By Ramprasad
I guess tat means that there are no unaligned...

I guess tat means that there are no unaligned reads..
Why dont you simulate some reads and cat them to your read files and then try??:)
Forum: Bioinformatics 11-10-2011, 03:36 AM
Replies: 0
Views: 1,891
Posted By Ramprasad
min-frags-per-transfrags option in cufflinks

Hi all,

I am goin to work with my first transcriptome data and I am planning to use cufflinks for RNA assembly.

I went through the manual and have a couple of queries :confused:

1)...
Forum: Bioinformatics 10-16-2011, 10:18 PM
Replies: 0
Views: 5,734
Posted By Ramprasad
n50 value for transcriptome assembly

Hi,
I am doing a Denovo transcriptome assembly using oases. I would like to know about the relation between n50 value obtained from velvet assembly and the performance of oases.
Generally...
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