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Search: Posts Made By: HenrivdGeest
Forum: Bioinformatics 04-12-2015, 12:40 PM
Replies: 2
Views: 1,373
Posted By HenrivdGeest
Thanks for your reply, and fix! How does soap3...

Thanks for your reply, and fix!
How does soap3 anyway performs compared to soap2 on cpu?
Forum: Pacific Biosciences 11-14-2013, 01:53 AM
Replies: 17
Views: 13,079
Posted By HenrivdGeest
Yes,I also encounter this. I think there is a...

Yes,I also encounter this.
I think there is a small bug in the sample scripts in the latest release of pbjelly(13.10.22). The mapping quality of the reads is lower than the default filtering...
Forum: Bioinformatics 09-23-2013, 12:15 AM
Replies: 26
Views: 17,213
Posted By HenrivdGeest
like the posters before me, you don't HAVE to buy...

like the posters before me, you don't HAVE to buy it :)

For me and for some colleagues CLC really is accelerating research. Its mostly the visualisation part that helps. I, as a bioinformatician...
Forum: Pacific Biosciences 06-27-2013, 11:29 PM
Replies: 17
Views: 13,079
Posted By HenrivdGeest
I've never tried pbjelly with clean reads. Since...

I've never tried pbjelly with clean reads. Since most of the time those reads will be shorter, the chance of finding an overlap is also smaller. If there aren't shorter, I would not see any drawback...
Forum: Pacific Biosciences 03-19-2013, 01:27 AM
Replies: 17
Views: 13,079
Posted By HenrivdGeest
I think you should look in the that output log...

I think you should look in the that output log file for "Didn't pass assembly". Those are the assemblies that failed. Could be due to the crash or due to another issue of which I am not aware of :)...
Forum: Pacific Biosciences 02-27-2013, 06:23 AM
Replies: 17
Views: 13,079
Posted By HenrivdGeest
If you run PBJelly, you run the mapping and the...

If you run PBJelly, you run the mapping and the assembly step separately, so you can change the code in between. Or make some if statement in the code itself:)
Forum: Pacific Biosciences 02-27-2013, 12:00 AM
Replies: 17
Views: 13,079
Posted By HenrivdGeest
Hi, I also got this error a few times. But,...

Hi,
I also got this error a few times.
But, its not that its not a problem. The errors you see come from an individual gap closure assembly operation. That one just failed. You can see these failed...
Forum: Academic/Non-Profit Jobs 02-13-2013, 07:26 AM
Replies: 0
Views: 1,852
Posted By HenrivdGeest
Bioinformatics Research Assistant

Will you become my new colleague?

url: http://www.academictransfer.com/17297/
@The Netherlands
@Wagingen
@Plant Research International

Job description

We are looking for a...
Forum: Bioinformatics 10-29-2012, 02:06 AM
Replies: 9
Views: 7,762
Posted By HenrivdGeest
Hello, I just tried LSC, and it looks good; ...

Hello,

I just tried LSC, and it looks good;
some remarks:

-input cant be fastq, at first I tried to run with fastq but run into weird errors and crashes.
- It cant handle multiline fasta...
Forum: Pacific Biosciences 09-21-2012, 02:20 AM
Replies: 31
Views: 15,395
Posted By HenrivdGeest
Thanks. I am indeed now only using 454 reads. I...

Thanks. I am indeed now only using 454 reads. I also have 454 paired end of 3KB, so that might also help with the long pacbio reads.
Forum: Pacific Biosciences 09-21-2012, 02:18 AM
Replies: 31
Views: 15,395
Posted By HenrivdGeest
Indeed, I am using the current cvs release, and...

Indeed, I am using the current cvs release, and it has this option with -maxGap.
I set it to 300 to allow pieces upto 300bp not having any coverage. It dit help, my median read length of the fixed...
Forum: Bioinformatics 07-09-2012, 10:43 AM
Replies: 5
Views: 3,465
Posted By HenrivdGeest
fastest way to 'parse' fasta or fastq?

I am looking for a real (High performace computing / HPC) fast fasta or fastq parsing program. I just want the most simple statistics imaginable:
- number of reads
- total nr of bases.
Other stuff...
Forum: Pacific Biosciences 07-05-2012, 09:31 AM
Replies: 31
Views: 15,395
Posted By HenrivdGeest
I did an Illumina only assembly, and that...

I did an Illumina only assembly, and that resulted in a 100MB contig file.And indeed, some areas have a bigger coverage than others. (some areas downto 1x)

I am now testing with a single pacbio...
Forum: Pacific Biosciences 07-05-2012, 05:25 AM
Replies: 31
Views: 15,395
Posted By HenrivdGeest
Can you be a bit more specific? - Is this...

Can you be a bit more specific?

- Is this already fixed in the downloadable binaries
- Do you have a url for this issue? (Can't find it on the wiki:...
Forum: Pacific Biosciences 07-05-2012, 04:44 AM
Replies: 31
Views: 15,395
Posted By HenrivdGeest
I also tried to run the pacbioToCa pipeline, but...

I also tried to run the pacbioToCa pipeline, but for our case it initially took 200days to complere (extrapolated off course!) . It turned out that we have a huge E.coli contamination, making the...
Forum: Introductions 02-15-2012, 10:27 PM
Replies: 0
Views: 1,567
Posted By HenrivdGeest
Smile Hello, I am Henri van de Geest [The Netherlands]

Hi,

I am a bioinformatician working at Wageningen UR, Plant Research International. Currently I am assisting other researchers with their research, mostly transforming data, building...
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