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Forum: Bioinformatics 06-01-2012, 02:17 AM
Replies: 7
Views: 1,403
Posted By Raj
Hi, I'm assuming they've been annotated and are...

Hi,
I'm assuming they've been annotated and are bacteria/virus.
You can use MAUVE, which can do the alignment of 2 or more genomes and there is an option output orthologues based on your cutoffs. ...
Forum: Bioinformatics 05-30-2012, 09:03 AM
Replies: 2
Views: 1,142
Posted By Raj
Hi, Thanks for getting back to me. I've...

Hi,
Thanks for getting back to me.

I've tried AVA, but its not really geared towards SNP discovery i.e. novel snps. Its a fair amount of manual scanning for novel snps, although for known snps...
Forum: Bioinformatics 05-29-2012, 09:21 AM
Replies: 2
Views: 1,142
Posted By Raj
SNP calling - all variants 454 data

Hi,
Apologies if this has been discussed previously, if so could you point me to the thread.

I've been given 454 data amplicon data, from which I would like to find SNPS, not just the dominant...
Forum: Bioinformatics 03-01-2012, 02:39 AM
Replies: 2
Views: 1,431
Posted By Raj
Question Haplotype discovery - 454 data

Hi,
I hope you can help.
I've been asked to search for novel haplotypes from a series of 454 sequenced amplicons.

I would like to know if there is any software that can search for potential...
Forum: 454 Pyrosequencing 07-21-2011, 01:45 AM
Replies: 0
Views: 850
Posted By Raj
Roche Junior - epigenomic project design

Hi,
I hope you can help.

We’re in the process of designing a sequencing project but am unsure if its feasible and if so how best to do it? (It will be done on the Roche Junior)

The aim is to...
Forum: 454 Pyrosequencing 05-11-2011, 08:33 AM
Replies: 27
Views: 9,707
Posted By Raj
Hi TonyBrooks, Thanks for getting back to me so...

Hi TonyBrooks,
Thanks for getting back to me so quickly!
I understand your point regarding the bioanalyser. I should have said that in addition we perform library quantitation using the...
Forum: 454 Pyrosequencing 05-11-2011, 06:30 AM
Replies: 27
Views: 9,707
Posted By Raj
Problem - Very low number of enriched beads

Hi,
Related to bead enrichment (for the Roche Junior), we're having the problem where we are not getting enough beads, essentially its looks like the vast majority of the beads is being lost. We're...
Forum: 454 Pyrosequencing 04-05-2011, 09:08 AM
Replies: 1
Views: 1,786
Posted By Raj
Alternatives to Roche Shotgun and PE protocol

Hi,
I hope you can help or give some pointers in the right direction. we've been working with Junior recently and have tried genome sequencing using the 8 kb pair end, it worked, which was nice :)...
Forum: 454 Pyrosequencing 04-05-2011, 08:34 AM
Replies: 1
Views: 1,838
Posted By Raj
Hi, This maybe a bit late, I was just browsing...

Hi,
This maybe a bit late, I was just browsing the 454 forum for something else...anyways, if its still of use:
For comparing scaffolds with a reference genome you can:
Use roche reference mapper...
Forum: 454 Pyrosequencing 01-16-2009, 08:51 AM
Replies: 12
Views: 5,923
Posted By Raj
I'm also using Fedora 10, in the 454 directory,...

I'm also using Fedora 10, in the 454 directory, if i run the application e.g. gsMapper from the directory 454/bin the GUI boots up.

If i go to via the apps directory, I get the command line...
Forum: 454 Pyrosequencing 01-16-2009, 03:32 AM
Replies: 12
Views: 5,923
Posted By Raj
Hi, I had a similar problem using fedora, the...

Hi,
I had a similar problem using fedora, the way i got it to work was to, set a couple of paths to the software, depending on what version you are using the paths will be different.

Version 1.X...
Forum: Bioinformatics 01-16-2009, 03:21 AM
Replies: 6
Views: 7,184
Posted By Raj
...I was informed yesterday that the new version...

...I was informed yesterday that the new version of consed (v18) should now be fully compatible with 454 data.
Also, with proposed release of Gap5, this too should also resolve the incompatibility...
Forum: Bioinformatics 01-08-2009, 01:51 AM
Replies: 6
Views: 7,184
Posted By Raj
Assembling .sff files from 454 and finishing

Hi can anybody suggest good assembly programs, other than Newbler and MIRA, which can use .sff files directly as an input file, not fasta.

Also, I have generated an .ace file from newbler which is...
Forum: De novo discovery 01-07-2009, 08:36 AM
Replies: 7
Views: 8,000
Posted By Raj
Hi, I've been working with much smaller...

Hi,
I've been working with much smaller genomes, bacterial approx. 4.5mb in size, 1.6million assembled reads. Using Newbler version 2.0, 64bit, checking the 'complex large genome' tab it took...
Forum: Bioinformatics 01-07-2009, 08:31 AM
Replies: 8
Views: 8,089
Posted By Raj
The programs i've used are MIRA and the newest...

The programs i've used are MIRA and the newest version of Newbler, i think there on version 2, which you should have with your instrument.

MIRA is completely free, runs on linux and is pretty good...
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