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Forum: Bioinformatics 05-28-2015, 10:32 PM
Replies: 1
Views: 1,362
Posted By JdeBruin
bcftools for finding unique SNP

Hi,

Would appreciated some help, I am a neophyte when it comes to dealing with vcf files.

I have 5 vcf files each represented a unique individual of the same species. I would like to filter the...
Forum: Bioinformatics 05-11-2015, 01:25 AM
Replies: 2
Views: 1,626
Posted By JdeBruin
I thanks, I am reading the VCF tools currently...

I thanks, I am reading the VCF tools currently and I have used it. Was wondering if anyone has an command example that would achieve this.
Forum: Bioinformatics 05-11-2015, 01:11 AM
Replies: 2
Views: 1,626
Posted By JdeBruin
Find common SNP in vcf files.

Hi,

I have vcf files for 6 individuals and I would like to find SNP's that occur in all 6 vcf files. Any ideas how this can be done, I can write a script to do this but if it is been done I don't...
Forum: Bioinformatics 11-24-2014, 08:39 PM
Replies: 0
Views: 870
Posted By JdeBruin
GAM-NGS Help

Hi,

I am trying to use GAM-NGS to merg two assemblies but I get the following error:
[error] the number of contigs loaded from the master fasta file is different from the number of sequences in...
Forum: Bioinformatics 08-14-2014, 05:36 AM
Replies: 7
Views: 1,505
Posted By JdeBruin
Yes I am referring to BLAST@NCBI. I have selected...

Yes I am referring to BLAST@NCBI. I have selected for blastn as this is what I have been using on the command line. I have had different dataset produce results just this particular set does not. I...
Forum: Bioinformatics 08-14-2014, 04:24 AM
Replies: 7
Views: 1,505
Posted By JdeBruin
This is my blast command: ...

This is my blast command:
~/apps/blast/bin/blastn -num_threads 15 -query query.fa -db /scratch/sysusers/jurgens/DB/nr -out qeury.blast.nr.out -outfmt "6 qseqid sseqid evalue qstart qend sstart send...
Forum: Bioinformatics 08-13-2014, 10:52 PM
Replies: 7
Views: 1,505
Posted By JdeBruin
Results form local blast installation

Hi,

I have a local BLAST installation on our cluster, I aslo have the nr database the uniprot and pfam. Currently I have a dataset that when I blast against the nr or uniprot tremble I get no...
Forum: Bioinformatics 08-12-2014, 12:31 AM
Replies: 0
Views: 1,497
Posted By JdeBruin
Abyss and OpenMPI

Hi All,

I have compiled abyss-1.5.2 with openmpi-1.8.2, take note my openmpi is in a non-standard location so I configure my build with " ./configure --with-boost=/usr/local/include...
Forum: Bioinformatics 07-24-2014, 05:49 AM
Replies: 2
Views: 2,170
Posted By JdeBruin
Extract flanking sequence of SNP call

Hi all.

I have mapped sequencing data to a reference using BWA and called SNP using samtools mpileup and generated a vcf using bcftools. What I would like to achieve is to extract the SNP along...
Forum: Bioinformatics 03-20-2014, 04:32 AM
Replies: 2
Views: 2,936
Posted By JdeBruin
CEGMA : Genewise Error

Hi all,

I am trying to run CEGMA and I am getting the following error message that has me lost:
Warning Error
Unable to open gene.stat as gene stats file
Warning Error
Could...
Forum: Bioinformatics 02-13-2014, 03:21 AM
Replies: 4
Views: 2,593
Posted By JdeBruin
SNP calling on low coverage NGS data

Hi,

I am new to SNP calling and would appreciate some input. I want to try and call SNP's for a specific organisms. The hurdles I have is, I do not have a reference genome to map against and I...
Forum: Bioinformatics 12-05-2013, 01:31 AM
Replies: 7
Views: 2,486
Posted By JdeBruin
I have been able to solve the problem

I have been able to solve the problem
Forum: Bioinformatics 12-04-2013, 09:03 PM
Replies: 7
Views: 2,486
Posted By JdeBruin
Hi, when I use the following: samtools...

Hi,

when I use the following:
samtools view indexed_sorted.bam chr2:1,000,000-2,000,000
I get the following error:
[bam_header_read] EOF marker is absent. The input is probably truncated....
Forum: Bioinformatics 12-03-2013, 08:39 PM
Replies: 7
Views: 2,486
Posted By JdeBruin
Thanks for all the solutions!!

Thanks for all the solutions!!
Forum: Bioinformatics 12-03-2013, 12:43 AM
Replies: 7
Views: 2,486
Posted By JdeBruin
Hi thanks for the reply. The gaps can be...

Hi thanks for the reply.

The gaps can be seen in the mapping results using IGV/picard thus the gaps can be defined.
Forum: Bioinformatics 12-02-2013, 09:38 PM
Replies: 7
Views: 2,486
Posted By JdeBruin
Extract Mapped Reads grouped by positions

Hi,

I have mapped reads to a reference genome using Bowtie2 and BWA, using samtools I have created bam files etc.

What I would like to achieve is to group reads based on the mapping location,...
Forum: Illumina/Solexa 06-04-2013, 03:54 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
Hey, I have used the RH installed zlib I...

Hey,

I have used the RH installed zlib I have also downloaded the latest zlib from zlib.org and compiled from source.

Probably have to uninstall all zlib and start over?
Forum: Illumina/Solexa 06-04-2013, 03:45 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
I have done so and I am still unable to "make"...

I have done so and I am still unable to "make" succesfully.

Error:

/root/apps/tmp_samtools/samtools-0.1.19/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':...
Forum: Illumina/Solexa 06-04-2013, 03:35 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
Hi will do so

Hi will do so
Forum: Illumina/Solexa 06-03-2013, 09:12 PM
Replies: 27
Views: 9,567
Posted By JdeBruin
Hi, Yes I have installed both: Version :...

Hi,

Yes I have installed both:
Version : 1.2.3 Vendor: Red Hat, Inc.
Forum: Illumina/Solexa 06-03-2013, 09:36 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
Samtools fails to build, the configure pass no...

Samtools fails to build, the configure pass no problem but the make command fails.
Forum: Illumina/Solexa 06-03-2013, 04:31 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
Yes I get the error when samtools are being build...

Yes I get the error when samtools are being build as part of a Casava installation.
I found libbam.a in opt/samtools-0.1.8/ but I believe due to the fact that the error is produced while samtools...
Forum: Illumina/Solexa 06-03-2013, 04:16 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
This is indeed a RHEL 6.x system I have not...

This is indeed a RHEL 6.x system

I have not done as suggested with "libbam.a" is this included in the Casava dir?

Thanks
Forum: Illumina/Solexa 06-03-2013, 03:22 AM
Replies: 27
Views: 9,567
Posted By JdeBruin
I do hope someone can help me with this I am...

I do hope someone can help me with this I am trying to install Casava 1.8.2 on a Red Hat Server. I have installed all the requirements as stated in the guide.

I get the following error:
...
Forum: Introductions 06-03-2013, 03:15 AM
Replies: 0
Views: 981
Posted By JdeBruin
Introductions

Hi I am a Bioinformatician I live in South Africa. I am fairly New to NGS etc.

Thanks for a great forum
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