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Forum: Bioinformatics 10-04-2016, 01:38 AM
Replies: 0
Views: 843
Posted By v_kisand
Xander assembler

Dear all,

seems there hasn't been any discussion about Xander https://github.com/rdpstaff/Xander_assembler in seqanswers. And very little is found in web in general. My questions is does anybody...
Forum: Illumina/Solexa 09-18-2015, 02:06 AM
Replies: 3
Views: 1,587
Posted By v_kisand
if you have a good enough reference genome, map...

if you have a good enough reference genome, map all reads with low stringency to reference and filter out region of interest. Only it is hard to see the scientific idea behind this...
Forum: Bioinformatics 09-15-2015, 11:57 PM
Replies: 0
Views: 911
Posted By v_kisand
Illumina amplicon sequencing and singletons

hi SEQanswers,

I have a question about ssu rRNA gene fragment analysis when the amplicons are sequenced on NGS. In old times when we had 454 data, a singleton was considered to be 1 unique...
Forum: Bioinformatics 11-15-2013, 05:59 AM
Replies: 8
Views: 4,184
Posted By v_kisand
yes, kind a physical mapping, not long contigs...

yes, kind a physical mapping, not long contigs are expected. And at this phase I _do not want_ any assemblies, even when possible, between reads from separate files
Forum: Bioinformatics 11-15-2013, 05:38 AM
Replies: 8
Views: 4,184
Posted By v_kisand
yap, thanks for quick reply! I learned the same...

yap, thanks for quick reply! I learned the same while finally checking velveth -help, lazy me... But strangely there is nothing about these switches in manual.

so the only way would be piping...
Forum: Bioinformatics 11-15-2013, 04:48 AM
Replies: 8
Views: 4,184
Posted By v_kisand
I have a similar but a bit different issue. I...

I have a similar but a bit different issue. I have thousands of regions over genome sequenced. These reads (single-end) are clustered into separate files (fastq). How to use velvet to assemble these...
Forum: Bioinformatics 01-26-2013, 06:36 AM
Replies: 7
Views: 3,196
Posted By v_kisand
I guess you should first check - do you run...

I guess you should first check - do you run consed from an edit_dir folder and that you have a phd_dir folder at the same level as edit_dir..

and just a recommendation do not use root as default...
Forum: Bioinformatics 11-02-2011, 10:30 PM
Replies: 4
Views: 2,461
Posted By v_kisand
assembly of metagenomic reads should be useful...

assembly of metagenomic reads should be useful for some other purposes, not for reducing workload...:-) Getting full genes, maybe even some operons, Easier do to recruitment maps. However I would not...
Forum: Bioinformatics 11-02-2011, 06:11 AM
Replies: 4
Views: 2,461
Posted By v_kisand
why you want to skip quality data? That is not a...

why you want to skip quality data? That is not a good idea, never :-) Homopolymers are the problem in 454 data anyway ...

Isn't mothur good for deep sequencing data of similar, kind a marker...
Forum: Bioinformatics 11-02-2011, 05:58 AM
Replies: 7
Views: 3,196
Posted By v_kisand
never tried before but seems Geneious produces...

never tried before but seems Geneious produces bad ace file. My error message is following:

exception thrown: ace file error detected from source file parseAceFile.cpp at 1907
Error in file...
Forum: Bioinformatics 11-02-2011, 05:21 AM
Replies: 1
Views: 1,637
Posted By v_kisand
perhaps SRS? http://www.ncbi.nlm.nih.gov/sra...

perhaps SRS?

http://www.ncbi.nlm.nih.gov/sra

-veljo
Forum: Bioinformatics 11-02-2011, 05:16 AM
Replies: 9
Views: 3,463
Posted By v_kisand
Nick has a good blog, I would go for MIRA3. ...

Nick has a good blog, I would go for MIRA3.

-veljo
Forum: Academic/Non-Profit Jobs 09-24-2010, 12:48 AM
Replies: 0
Views: 1,872
Posted By v_kisand
Post doc on environmental genomics/metagenomics

I am looking for post doc (2 years + option to extend 1 year) on the area of de novo bacterial genome assembly and downstream analysis of these data using NGSs (454 and Illumina), also analysis of...
Forum: Bioinformatics 09-21-2010, 01:55 AM
Replies: 6
Views: 2,356
Posted By v_kisand
as kind a intermediate user myself seg fault...

as kind a intermediate user myself seg fault means to me there is installation/compilation error... usually compilation from source will help.

reasonable pace.... hmmm with my modest Intel(R)...
Forum: Sample Prep / Library Generation 09-16-2010, 10:35 PM
Replies: 5
Views: 2,158
Posted By v_kisand
there are some more threads concerning DNA but...

there are some more threads concerning DNA but I just write my experience here:

in most cases it is possible to get things working but I doubt that you know _exact_ concentration of DNA (e.g....
Forum: Sample Prep / Library Generation 09-16-2010, 05:00 AM
Replies: 3
Views: 2,724
Posted By v_kisand
no clue in this case, sry...

no clue in this case, sry...
Forum: Sample Prep / Library Generation 09-16-2010, 04:55 AM
Replies: 3
Views: 2,686
Posted By v_kisand
I am afraid none of them is reliable. When...

I am afraid none of them is reliable. When possible use the most conservative value.
Forum: Sample Prep / Library Generation 09-16-2010, 04:52 AM
Replies: 5
Views: 2,158
Posted By v_kisand
Meanwhile we tried to increase amount of DNA for...

Meanwhile we tried to increase amount of DNA for Rapid Kit and so far results improved!
Only explanation I have, DNA quantification is always a bit problematic issue...
Forum: 454 Pyrosequencing 09-16-2010, 04:33 AM
Replies: 9
Views: 13,529
Posted By v_kisand
And also check Hong, S.-H, Bunge, J., Leslin,...

And also check
Hong, S.-H, Bunge, J., Leslin, C., Jeon, S-O., and Epstein, S. S. (2009). Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME Journal (advanced on-line...
Forum: Bioinformatics 09-16-2010, 04:20 AM
Replies: 2
Views: 1,715
Posted By v_kisand
I guess you mean human genome... well I work with...

I guess you mean human genome... well I work with almost exclusively with bacteria but I do not see any advantage in de novo sequencing over reference mapping. you have to be really sure that you...
Forum: Sample Prep / Library Generation 08-04-2010, 05:53 AM
Replies: 5
Views: 2,158
Posted By v_kisand
454 Rapid kit in metgenomics

Hi all,

We use Roche Rapid kit for environmental metagenomics. People working in this area probably have experienced that total community DNA is usually not with as highly good quality as...
Forum: Sample Prep / Library Generation 08-04-2010, 05:42 AM
Replies: 3
Views: 2,724
Posted By v_kisand
meaning no library or later no reads when...

meaning no library or later no reads when sequencing?

v.
Forum: Bioinformatics 02-03-2010, 05:28 AM
Replies: 78
Views: 44,714
Posted By v_kisand
I just compiled b4 release and it works like a...

I just compiled b4 release and it works like a charm,

I was wondering about gap2caf, caf2baf etc. tools. I experience some difficulties in compiling original cap2caf from source code. How one...
Forum: Bioinformatics 01-26-2010, 10:40 PM
Replies: 27
Views: 12,384
Posted By v_kisand
hmm, looks like C++ problem... othrewise I...

hmm, looks like C++ problem...

othrewise I run
./configure --with-Qt-dir= ...

Qt is used for GUIs even when qt3.3 is missing or not directed, the compilation runs fine, non-GUI part will...
Forum: Bioinformatics 01-26-2010, 01:43 AM
Replies: 27
Views: 12,384
Posted By v_kisand
I guess what you need is: some modified .cc...

I guess what you need is:

some modified .cc files from Ariadna Rodriguez Chamorro (ariadna dot rodriguez at unil dot ch).

when you drop your E-mail I can send these replacements

What I...
Showing results 1 to 25 of 37

 


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