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Forum: Illumina/Solexa 02-28-2014, 05:48 AM
Replies: 5
Views: 4,324
Posted By Shlomo Blum
How? Could you share a protocol or reference?

How? Could you share a protocol or reference?
Forum: Bioinformatics 10-30-2013, 05:47 AM
Replies: 2
Views: 1,329
Posted By Shlomo Blum
Pseudo-molecule

Hi,

How may I concatenate contigs into a single pseudo-molecule using a linker sequence? Does anyone know of a script for this purpose?
Forum: Bioinformatics 06-01-2013, 09:09 PM
Replies: 21
Views: 11,636
Posted By Shlomo Blum
Koadman: so to get a single pseudo-genome from...

Koadman: so to get a single pseudo-genome from the mauve output one would only need to add N's between the ordered contigs and separate the unaligned contigs?
Forum: Bioinformatics 06-01-2013, 09:07 PM
Replies: 21
Views: 11,636
Posted By Shlomo Blum
Exited with error code: -1073741819

Could anyone help me on this error?

Searching with seed pattern 11110011010101011001111
Sorted mer list loaded successfully
Sorted mer list loaded successfully...
Forum: Bioinformatics 06-01-2013, 08:47 PM
Replies: 3
Views: 810
Posted By Shlomo Blum
Do these tools work with prokaryote genomes? ...

Do these tools work with prokaryote genomes?

Actually, I would like to compare gene by gene annotation from each source and not only to compare overall quality.

While PGAAP output comes ready...
Forum: Bioinformatics 06-01-2013, 04:33 AM
Replies: 3
Views: 810
Posted By Shlomo Blum
annotation merge

Hi,

I would like to compare the annotation of a bacterial draft genome made by two different pipelines (PGAAP and RAST).

Any ideas how to do that?

Is it possible to "merge" the annotations...
Forum: 454 Pyrosequencing 05-21-2013, 07:41 AM
Replies: 0
Views: 1,138
Posted By Shlomo Blum
Finishing Scripts V1.0

Hello,

I recently found this paper:

Nagarajan et al., Finishing genomes with limited resources: lessons from an ensemble of microbial genomes BMC Genomics 2010, 11:242.
doi:...
Forum: De novo discovery 02-16-2013, 01:25 PM
Replies: 0
Views: 948
Posted By Shlomo Blum
Pseudocontig and annotation transfer

Hello,

I have a couple of bacterial strains sequenced using 454 and assembled de novo. I aligned the contings to a ref. strain using Contiguator and got one pseudocontig for each strain.

How...
Forum: Bioinformatics 11-25-2012, 09:28 PM
Replies: 4
Views: 2,076
Posted By Shlomo Blum
They are the same species, but not the same...

They are the same species, but not the same phylogeny. Anyway, even if mapping to a reference, the idea is to assemble de novo whatever remains unmapped.

The point is, how much a difference does...
Forum: Bioinformatics 11-25-2012, 10:03 AM
Replies: 4
Views: 2,076
Posted By Shlomo Blum
Nothing, eh? I'm working with bacterial...

Nothing, eh?

I'm working with bacterial genomes, and although I have plenty of refs out there (E. coli...), I still wonder what's best, de novo or mapping, since we aim to search for novel genes....
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