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Search: Posts Made By: joa_ds
Forum: Bioinformatics 12-17-2010, 05:20 AM
Replies: 3
Views: 1,544
Posted By joa_ds
Well, Back in the old days (like 1 year ago...

Well,

Back in the old days (like 1 year ago or so...) the basecaller produces two sets of fasta files. TCA.fa and ATG.fa if I remember correct. One file was the real file, the other one with...
Forum: Bioinformatics 12-17-2010, 01:53 AM
Replies: 8
Views: 1,972
Posted By joa_ds
drop me an email @ joachim dot deschrijver at...

drop me an email @ joachim dot deschrijver at ugent dot be

I have such a script ready in Perl that you could use
Forum: Bioinformatics 12-16-2010, 06:04 AM
Replies: 3
Views: 1,544
Posted By joa_ds
454 CWF files

Hi fellow sequence analysts.

I am working on a 454 basecalling project and I have 2 main questions/problems.

1) It really would help me if someone could tell me a method to get the controlbead...
Forum: Bioinformatics 11-30-2010, 06:04 AM
Replies: 1
Views: 1,153
Posted By joa_ds
Abyss-PE error

Hi community,

I am currently involved in a rather complex project where we are hunting for causal SNPs in a species that has no assembled genome at the moment. We are planning on sequencing some...
Forum: Bioinformatics 06-25-2010, 06:19 AM
Replies: 16
Views: 2,290
Posted By joa_ds
i feel stupid now... but thx for the hint :)

i feel stupid now...

but thx for the hint :)
Forum: Bioinformatics 06-25-2010, 05:15 AM
Replies: 16
Views: 2,290
Posted By joa_ds
I happen to have some problems using BWA ... I...

I happen to have some problems using BWA ... I really need to index short reads (i.e. 16S RNA).

I understand i need to install the additional package. So I installed it, but still an error.
...
Forum: Bioinformatics 05-27-2010, 03:35 AM
Replies: 5
Views: 803
Posted By joa_ds
I'm glad to see people actually using the VIP...

I'm glad to see people actually using the VIP pipeline.

We have been using the pipeline internally for almost a year now. But eventually, some bug will appear here and there. Please report any bug...
Forum: Bioinformatics 05-27-2010, 02:28 AM
Replies: 7
Views: 1,712
Posted By joa_ds
I just checked out their site and found the...

I just checked out their site and found the following thing.

SOAPindel: SOAPindel is developed to find the insertion and deletion specially for re-sequence technology : Coming soon.

I am just...
Forum: Bioinformatics 05-27-2010, 01:56 AM
Replies: 7
Views: 1,712
Posted By joa_ds
Well, I can tell you the following. I have...

Well, I can tell you the following.

I have simulated loads of data. I have generated datasets with more than a billion reads where error profiles/PCR errors/sequencing errors were simulated and...
Forum: Bioinformatics 05-27-2010, 01:42 AM
Replies: 7
Views: 1,712
Posted By joa_ds
SOAP2 and deletions/insertions

I was told that SOAP should be able to detect deletions and insertions up to 3bp.

So i made a reference file and a file with a normal read and some reads with 1,2,3 bp deleted and inserted. Just...
Forum: Bioinformatics 04-23-2010, 03:54 AM
Replies: 10
Views: 5,485
Posted By joa_ds
Can you elaborate the experiment design a bit? ...

Can you elaborate the experiment design a bit?

Are you mapping genome-wide or just on coding regions? Human genome or a smaller species?

It would be strange, but correct me if I see it wrong,...
Forum: Bioinformatics 04-23-2010, 03:19 AM
Replies: 10
Views: 5,485
Posted By joa_ds
we did our first RNA seq run last week and the...

we did our first RNA seq run last week and the first results came back today. I have to admint that my collegeau did all the work, I just had some discussions with him and looked at some graphs he...
Forum: Bioinformatics 04-23-2010, 01:07 AM
Replies: 3
Views: 1,581
Posted By joa_ds
Abyss @ 454

Hi there,

Is ABYSS designed for assembly of 454 reads?


# ./ABYSS -k25 -o /data/454/data/_Test_assembly /data/454/data/2.TCA.454Reads.fna

gives me the following

2.TCA.454Reads.fa' is an...
Forum: Illumina/Solexa 04-14-2010, 07:09 AM
Replies: 28
Views: 8,563
Posted By joa_ds
thx a lot for the info ! I will let you know in...

thx a lot for the info ! I will let you know in some weeks if things worked out ok :o
Forum: Illumina/Solexa 04-14-2010, 01:56 AM
Replies: 28
Views: 8,563
Posted By joa_ds
I understand that the directional RNA seq on...

I understand that the directional RNA seq on illumina is only for mRNA? Is there a total RNA protocol/kit available somewhere?

I know SOLID has a total RNA directional sequencing kit, but i don't...
Forum: Bioinformatics 12-14-2009, 08:53 AM
Replies: 3
Views: 1,411
Posted By joa_ds
have you analysed your data further downstream ? ...

have you analysed your data further downstream ?

you are better off with 40% mapped sequences and good results than with 60% mapped rubbish.

what is the type of experiment you are doing at the...
Forum: 454 Pyrosequencing 12-14-2009, 07:14 AM
Replies: 7
Views: 1,400
Posted By joa_ds
I am currently using "gsRunProcessor 2.0.01.12". ...

I am currently using "gsRunProcessor 2.0.01.12".

For refiltering I follow the steps provided in the original manual @ page 56 and further.

Little summary of those pages:

gsRunProcessor...
Forum: 454 Pyrosequencing 12-13-2009, 02:42 PM
Replies: 7
Views: 1,400
Posted By joa_ds
I still have to install the new versions of the...

I still have to install the new versions of the software, so I cannot say what the cause of the 3-5% is.

But have you checked the standard filter values compared to the older software pipeline? I...
Forum: Genomic Resequencing 08-26-2009, 07:38 AM
Replies: 9
Views: 3,189
Posted By joa_ds
Well, linux has no .exe extensions. So trying to...

Well, linux has no .exe extensions. So trying to use that .exe bowtie will never work. You should get a linux version to run in your linux shell.
Forum: General 08-26-2009, 06:36 AM
Replies: 4
Views: 10,003
Posted By joa_ds
NAture Biotech: Next-Generation DNA sequencing...

NAture Biotech:
Next-Generation DNA sequencing by Jan Shendure and Hanlee Ji

Good luck
Forum: Genomic Resequencing 08-26-2009, 06:34 AM
Replies: 9
Views: 3,189
Posted By joa_ds
are you trying to use a bowtie.exe on a linux...

are you trying to use a bowtie.exe on a linux system?

You are probaly using the iTunes bowtie on a linux system.

Did you get bowtie from http://bowtie-bio.sourceforge.net/index.shtml?
Forum: 454 Pyrosequencing 08-26-2009, 06:32 AM
Replies: 15
Views: 6,387
Posted By joa_ds
hehe, we also tried amplicon sequencing on the...

hehe, we also tried amplicon sequencing on the Titanium. Poor results. Only 200k reads with poor quality. So should wait indeed for the titanium package.
Forum: Bioinformatics 08-12-2009, 12:31 AM
Replies: 33
Views: 11,589
Posted By joa_ds
Hi there, i am under some pressure to deliver...

Hi there, i am under some pressure to deliver results from a solexa run. They did a run, and all i had to do was give them a list of variants.

Problem is, i ran bowtie, give them the list. They...
Forum: Bioinformatics 08-10-2009, 07:04 AM
Replies: 18
Views: 11,407
Posted By joa_ds
hi there again... The reasons I am trying...

hi there again...

The reasons I am trying BWA (still hasn't worked... ) is because I am analyzing illumina data for counting variant frequencies for a pool of several patients.

So far so good,...
Forum: Bioinformatics 08-05-2009, 07:17 AM
Replies: 511
Views: 118,117
Posted By joa_ds
Isn't there a feature to export unmapped reads to...

Isn't there a feature to export unmapped reads to a file?

I always run bowtie and export unmapped and repeats using

--unfq unaligned.fastq --maxfa duplicates.fastq

taking a look at the size...
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