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Forum: Bioinformatics 01-03-2018, 12:55 AM
Replies: 2
Views: 1,181
Posted By stevebaeyen
de novo metatranscriptomics

Nobody willing to share advice on this subject?
Forum: Bioinformatics 12-22-2017, 04:46 AM
Replies: 2
Views: 1,181
Posted By stevebaeyen
de novo metatranscriptomics pipeline for soil

Hi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if...
Forum: Bioinformatics 11-27-2014, 04:59 AM
Replies: 11
Views: 7,500
Posted By stevebaeyen
Arrow Found a solution!! We adapted the script because...

Found a solution!! We adapted the script because there was an error counting the fragments. Here is the script (ran on Ubuntu 12,04 LTS):
#!/usr/bin/perl

### david.studholme@tsl.ac.uk

###...
Forum: Bioinformatics 11-25-2014, 06:41 AM
Replies: 11
Views: 7,500
Posted By stevebaeyen
Hi, I tried to use the fasta2agp.pl script but...

Hi,
I tried to use the fasta2agp.pl script but I get errors when submitting to NCBI WGS. The script is from 2010 and there is a new AGPv2,0 version since 2012. The script worked but there is an...
Forum: Bioinformatics 02-27-2013, 01:45 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
sivasubramani

Thank you for your excellent tips sivasubramani, but the problem is solved by now . I indeed used a very strict trimming, duplicate removal, etc. before doing de novo assembly wit a k-mer parameter...
Forum: Bioinformatics 08-01-2012, 12:05 AM
Replies: 2
Views: 1,213
Posted By stevebaeyen
SSR screening:better tools than RepeatFinder?

Hi ,
has anybody experience using SSR tools for repeat discovery in draft genomes? I will test Repeatfinder and Sputnik but I was wondering if there are other tools out there.
Thanks for helping...
Forum: Bioinformatics 02-08-2012, 09:35 AM
Replies: 4
Views: 1,562
Posted By stevebaeyen
firefox 2 chrome experiences?

Hi, I have been using Firefox for years. I heard the news about google only supporting mozilla for another 3 years, so i wondered if most bioinformatic tools that rely on firefox would still work or...
Forum: Bioinformatics 01-19-2012, 05:00 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
and can you give me with a link to a review...

and can you give me with a link to a review article about optical mapping ?
Forum: Bioinformatics 01-19-2012, 04:08 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
Hi , I tried to denovo assemble PE+MP datasets on...

Hi , I tried to denovo assemble PE+MP datasets on the new CLC scaffolder but didn't get a huge improvement compared to the PE dataset alone. A succesfull scaffolding with a +/-70% reduction was...
Forum: Bioinformatics 12-23-2011, 02:36 AM
Replies: 5
Views: 3,119
Posted By stevebaeyen
We just finished a bacterial genome of 4.2Mb ...

We just finished a bacterial genome of 4.2Mb with 91x coverage 50bp paired-end reads and 60x 75bp 5kb mate-pair reads. After the paired-ends, we obtained 480 contigs (>200bp) after denovo assembly....
Forum: Bioinformatics 12-15-2011, 04:14 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
Hi Boetsie, thanks for the advice of using...

Hi Boetsie,
thanks for the advice of using SOAP's GapCloser ! Using the PE reads, i was able to close 161 of 400 gaps (of N's) in the scaffolds. Do you think the performance of Gapfiller would be...
Forum: Bioinformatics 12-14-2011, 05:54 AM
Replies: 5
Views: 1,855
Posted By stevebaeyen
how to get IMAGE2 running ?

I tried using IMAGE2 but there is no 'readme' or 'install' file and I can't find any information that explains how to install the software. I tried to run IMAGE2 on the example provided with the...
Forum: Bioinformatics 12-14-2011, 05:47 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
Wink IMAGE2 gap closing

Hi Boetsie,
we obtained very nice scaffolds using your SSPACE Premium v2 software (up to 937kb and N50=275kb). I tried using IMAGE2 but there is no 'readme' or 'install' file and I can't find any...
Forum: Bioinformatics 12-13-2011, 03:40 AM
Replies: 252
Views: 98,568
Posted By stevebaeyen
k-mers and m parameter

Dear Boetsie,
does this mean that we should have better results with the -m parameter optimised for k-mer size instead of read length ? How can we know the k-mer size used and how do we best adjust...
Forum: Bioinformatics 12-07-2011, 12:08 PM
Replies: 2
Views: 1,912
Posted By stevebaeyen
Wink soapdenovo gapcloser

Hi, you have to follow the 4-step assembly of soapdenovo as described on the Soapdenovo website instead of using the all command. In the last step (scaffolding) you can enter the -F parameter and...
Forum: Bioinformatics 11-29-2011, 07:16 AM
Replies: 2
Views: 1,912
Posted By stevebaeyen
any news?

same problem here, the manual is very cryptic...
Forum: Bioinformatics 11-28-2011, 05:43 AM
Replies: 17
Views: 7,973
Posted By stevebaeyen
scaffolding GAII paired-end library with Hiseq mate-pairs

Hello,
we are a Belgian research team studying the +/- 4Mbp genome of a bacterial plant pathogen (and newbies in NGS data analysis). We are getting some unexpected results during de novo assembly...
Forum: Introductions 08-19-2011, 04:10 AM
Replies: 0
Views: 1,482
Posted By stevebaeyen
Thumbs up Hello SEQanswers!

Hi,
my name is Steve Baeyen and since last year, I am working on genome assembly and comparative genomics of bacterial plant pathogens in the Institute for Fisheries and Agricultural Research...
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