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Forum: Bioinformatics 05-06-2013, 11:24 PM
Replies: 2
Views: 4,726
Posted By jjk
I am not sure if you still have the problem but...

I am not sure if you still have the problem but for people that will have the problem in the future...

When combining rnammer and hmmsearch keep in mind at least for me that hmmsearch 3.0 was not...
Forum: Illumina/Solexa 04-12-2013, 02:01 PM
Replies: 3
Views: 1,220
Posted By jjk
I will look up the exact procedure but what I...

I will look up the exact procedure but what I found out so far is that of the 5.700.000 reads 290.000 of them had this odd result. Which is 5% of the total amount of reads. Would this be a lot if...
Forum: Illumina/Solexa 04-12-2013, 11:42 AM
Replies: 3
Views: 1,220
Posted By jjk
Merged illumina data

I encountered something rather odd and I am not certain that this is an illumina artefact or that it is true what I see.

I was curious if it is possible that when working with RNA sequences, is...
Forum: Bioinformatics 01-30-2013, 10:46 PM
Replies: 2
Views: 3,002
Posted By jjk
GPU CUDA BLAST Efficiency

I am currently in the possession of the following:

7x CPU
16 GB memory

and a GeForce GTX 670 GPU
http://www.geforce.com/hardware/desktop-gpus/geforce-gtx-670/specifications

Now I was...
Forum: Bioinformatics 11-27-2012, 01:01 AM
Replies: 1
Views: 1,680
Posted By jjk
Keep BLASTdb in memory

As I am trying to set up a BLAST server I stumbled across a tiny "problem".

In the future I will do many tiny blasts of a few sequences at a time from different scripts and such. Is it possible to...
Forum: Bioinformatics 11-15-2012, 11:37 PM
Replies: 0
Views: 1,940
Posted By jjk
glimmer3 output

Currently I am setting up DIYA and I experienced some small problems with glimmer. I managed to install tigr-glimmer on ubuntu 12.10. Currently using g3-from-scratch.diya.csh to find ORF and now I am...
Forum: Bioinformatics 11-15-2012, 10:35 PM
Replies: 26
Views: 13,314
Posted By jjk
gcc -v Using built-in specs. ...

gcc -v
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc-4.7.real
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.7/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v...
Forum: Bioinformatics 11-15-2012, 08:43 AM
Replies: 26
Views: 13,314
Posted By jjk
Unfortunately I wasn't so lucky. I am running...

Unfortunately I wasn't so lucky. I am running ubuntu 12.10 but cant compile it whatsoever. I found out that there is a package called tigr-glimmer3. As I havent been able to run it yet, still looking...
Forum: RNA Sequencing 10-03-2011, 03:14 AM
Replies: 3
Views: 2,587
Posted By jjk
Hello, Thanks for the reply, you mean using...

Hello,

Thanks for the reply, you mean using coverageBed?

Am now at the positiion of coverageBed -a bedfile.bed but the tutorial talks about 10kb? how to do this for each nucleotide? Sorry for...
Forum: RNA Sequencing 10-03-2011, 02:29 AM
Replies: 3
Views: 2,587
Posted By jjk
Coverage per nucleotide

We have a mapped RNA-seq but now we want to know how many reads are mapped on each nucleotide in a genome. We went through many many many programs but we were only able to view the results in no...
Forum: RNA Sequencing 09-30-2011, 07:41 AM
Replies: 1
Views: 2,683
Posted By jjk
Reply to anyone who has found this through...

Reply to anyone who has found this through searching and was facing the same problem

Generating bam file
~/Apps/samtools-0.1.18/samtools view -bS xxx.sam > xxx.bam

Sorting...
Forum: RNA Sequencing 09-30-2011, 06:22 AM
Replies: 1
Views: 2,683
Posted By jjk
bowtie assembly on RNA seq viewer

Hello,

Just did a bowtie assembly on RNAseq data, checked in tablet all looks fine but is there a way to find out the coverage for each nucleotide in the genome file?

Thanks,
Forum: Bioinformatics 03-23-2010, 05:28 AM
Replies: 5
Views: 2,037
Posted By jjk
Through artemis i got the ORF's and through Run >...

Through artemis i got the ORF's and through Run > Pfam Search i get the correct name for the ORF. But how to do this for all my ORF's and automatically?

Found the readme.. (my bad)

Searching...
Forum: Bioinformatics 03-23-2010, 03:58 AM
Replies: 5
Views: 2,037
Posted By jjk
Thanks im looking into it at the moment. But does...

Thanks im looking into it at the moment. But does this program need a database located at our place or is NCBI also possible for mass blasting of all the ORF's and annotation. Still reading the...
Forum: Bioinformatics 03-22-2010, 11:55 PM
Replies: 5
Views: 2,037
Posted By jjk
Looking for Annotation software

At the moment i have more or less a chloroplast genome assembled. What i could do now is get al the ORF's and blast it and obtain the names by using for example BLAST2GO. The problems i am facing...
Forum: Bioinformatics 12-14-2009, 09:33 PM
Replies: 2
Views: 3,232
Posted By jjk
Tried bwa, but it gives an: ...

Tried bwa, but it gives an:

BWTIncConstruct() : Not enough memory allocated!

probably due to the fact that i ran it on my laptop with only 2gb in there i think. But thanks for the fast reply...
Forum: Bioinformatics 12-14-2009, 09:03 PM
Replies: 2
Views: 3,232
Posted By jjk
Bowtie with gaps

Searched almost all the day and only found 1 candidate that could match bowite a little bit. Im trying to find a short sequence aligner (illumina data set in fasta format) that allows gaps up to a...
Forum: Bioinformatics 12-13-2009, 08:22 PM
Replies: 0
Views: 907
Posted By jjk
Genome A tags Genome B

Already posted some questions about how to use different programs in this forum and the help was really appreciated but i think i should explain what i want to achieve because maybe i am on the wrong...
Forum: Bioinformatics 12-10-2009, 07:06 PM
Replies: 6
Views: 8,643
Posted By jjk
Genome coverage

I used bowtie to create sam files that are loaded in a tablet program for chloroplast assembly by tags. I guess there is an overall coverage of about 80%. But is there a way to let the program...
Forum: Bioinformatics 11-16-2009, 02:43 PM
Replies: 2
Views: 1,708
Posted By jjk
Tablet

For the people who don't know what to do with the .sam files like i did in the beginning. I found this program

http://bioinf.scri.ac.uk/tablet/

From the Plant Bioinformatics Group SCRI - Tablet...
Forum: Bioinformatics 11-15-2009, 05:55 PM
Replies: 2
Views: 1,708
Posted By jjk
New to Bowtie

I am pretty new when it comes to bioinformatics. But i need to use bowtie to do only one thing for me. I have multiple tags in a fasta file and i would like to align this against a genome.

Already...
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