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Forum: Bioinformatics 06-11-2013, 06:54 AM
Replies: 147
Views: 58,191
Posted By tonio100680
After use samtools sam2pindel then I execute...

After use samtools sam2pindel then I execute Pindel. Here is what I get ....



Do you have any idea?

Thank you in advance for your help
Forum: Bioinformatics 06-11-2013, 06:54 AM
Replies: 9
Views: 5,623
Posted By tonio100680
After use samtools sam2pindel then I execute...

After use samtools sam2pindel then I execute Pindel. Here is what I get ....



Do you have any idea?

Thank you in advance for your help
Forum: Bioinformatics 01-31-2013, 02:08 AM
Replies: 34
Views: 10,151
Posted By tonio100680
CONTRA help

Hello,

I am a junior bioinformatician! I have to implement CONTRA in laboratory. We work from a target catch (Agilent SureSelect).
For now I installed on a DEBIAN virtual machine CONTRA...
Forum: Bioinformatics 01-31-2013, 02:07 AM
Replies: 18
Views: 7,162
Posted By tonio100680
CONTRA help

Hello,

I am a junior bioinformatician! I have to implement CONTRA in laboratory. We work from a target catch (Agilent SureSelect).
For now I installed on a DEBIAN virtual machine CONTRA...
Forum: Bioinformatics 10-30-2012, 12:35 AM
Replies: 9
Views: 6,298
Posted By tonio100680
Hi all, I am currently looking for a...

Hi all,

I am currently looking for a software to determine CNV. Knowing that I am using data re-targeted sequencing (approximately twenty genes). I tested CONTRA but I would know your opinion?...
Forum: Bioinformatics 10-29-2012, 07:55 AM
Replies: 2
Views: 3,186
Posted By tonio100680
CNV detection and annotation

Hi all,

I am currently looking for a software to determine CNV. Knowing that I am using data re-targeted sequencing (approximately twenty genes). CONTRA I could but I would know your opinion? What...
Forum: Bioinformatics 10-29-2012, 07:53 AM
Replies: 9
Views: 6,298
Posted By tonio100680
Hi all, I am currently looking for a...

Hi all,

I am currently looking for a software to determine CNV. Knowing that I am using data re-targeted sequencing (approximately twenty genes). I tested CONTRA but I would know your opinion?...
Forum: Bioinformatics 06-13-2012, 11:10 PM
Replies: 0
Views: 1,500
Posted By tonio100680
snps & indels.txt CASAVA Illumina

Hi all,

I use the CASAVA pipeline with a GAIIx sequencer. Output, I get the BAM files and snps.txt and indels.txt. I try to convert these txt files into vcf file. I tested variationtoolkit but it...
Forum: Bioinformatics 01-12-2012, 06:33 AM
Replies: 7
Views: 4,770
Posted By tonio100680
Yet what I did (hg19_alias.tab): chr1.fa chr1 ...

Yet what I did (hg19_alias.tab):
chr1.fa chr1
chr2.fa chr2
chr3.fa chr3
chr4.fa chr4
chr5.fa chr5
chr6.fa chr6
chr7.fa chr7
chr8.fa chr8
chr9.fa chr9
Forum: Bioinformatics 01-12-2012, 05:13 AM
Replies: 7
Views: 4,770
Posted By tonio100680
I tested with your genomes (hg19 and b37) and I...

I tested with your genomes (hg19 and b37) and I get the same results (ie none). My chromosomes name : chr17.fa for example.
Should we merge the . bam files (one per chromosome) ?
Forum: Bioinformatics 01-11-2012, 06:32 AM
Replies: 7
Views: 4,770
Posted By tonio100680
No, I have Internet access. The .Bam files (one...

No, I have Internet access. The .Bam files (one per chromosome generated by CASAVA) should be merged (merge samtools)?
Forum: Bioinformatics 01-11-2012, 01:52 AM
Replies: 7
Views: 4,770
Posted By tonio100680
IGV - Genome problems

Hello,

I want to use IGV to see my GAIIx data (CASAVA v1.8). I import my bam files(.bam and .bam.bai) in IGV. I have to use a different genome because I can see my data. I imported the genome...
Forum: Bioinformatics 12-20-2011, 06:48 AM
Replies: 27
Views: 12,371
Posted By tonio100680
% On-Off target

hello,
I'm looking for a tool (or command line) to determine the % On-Off target + or - 50 bp of exon from my capture file but not annotated (!!!). Capture SureSelect agilent home.

Current...
Forum: Bioinformatics 08-18-2011, 05:36 AM
Replies: 3
Views: 2,977
Posted By tonio100680
CASAVA v1.8 with indels

My Settings :

Biology : GAIIx, SureSelect capture, paired-end 2x76 with "in house" indexing

BioInformatics : CASAVA v1.8 with ELANDv2, GenomeStudio

My problem :

One patient had a deletion...
Forum: Bioinformatics 08-18-2011, 02:35 AM
Replies: 2
Views: 7,382
Posted By tonio100680
samtools & flagstat & awk

Hi,
Here is my command :
$ samtools merge L002_LBCO1.bam L002_LBCO1_chr*.bam

$ samtools view L002_LBCO1.bam | awk '$3== "chr1.fa" && $4>= 45787123 && $4<= 45787316 || $3== "chr1.fa" && $4>=...
Forum: Bioinformatics 07-19-2011, 06:44 AM
Replies: 65
Views: 16,653
Posted By tonio100680
Dear Peter, For the first question : R is...

Dear Peter,

For the first question : R is installed in another folder (/opt /R/) and NGSrich is installed in folder : /stockage/tools/NGSrich_0.4.5
For the second question : my webbroswer...
Forum: Bioinformatics 07-19-2011, 02:19 AM
Replies: 65
Views: 16,653
Posted By tonio100680
Dear Peter, I am a beginner in the field of...

Dear Peter,
I am a beginner in the field of bioinformatics! How can I view my results in the "Data" (resulting files: align_LBC03_enrichment.bed align_LBC03_enrichment.xml align_LBC03_onTarget.wig...
Forum: Bioinformatics 07-19-2011, 02:12 AM
Replies: 65
Views: 16,653
Posted By tonio100680
Dear Peter, Thanks for help ! I...

Dear Peter,

Thanks for help !

I downloaded the new version. I use this command:

java NGSrich summarize -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -o...
Forum: Bioinformatics 07-19-2011, 12:30 AM
Replies: 65
Views: 16,653
Posted By tonio100680
Hi, My command : ...

Hi,

My command :

[ngs@s-ngs-client-linux tools]$ java NGSrich -r /stockage/ngs-client-01/tools/samtools/test_target/sam/align_LBC03.sam -a...
Forum: Literature Watch 07-08-2011, 01:43 AM
Replies: 46
Views: 41,620
Posted By tonio100680
Hi, how to view the level of a gene in...

Hi,

how to view the level of a gene in CNV-seq ?

Script :
samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
samtools view...
Forum: Bioinformatics 06-07-2011, 11:48 PM
Replies: 14
Views: 10,885
Posted By tonio100680
That's right, I want to use CASAVA 1.7 because...

That's right, I want to use CASAVA 1.7 because the 1.8 is not available in France...
I can not use novobarcode because the output format is not compatible with the input format CASAVA so I'm...
Forum: Bioinformatics 06-07-2011, 11:21 PM
Replies: 14
Views: 10,885
Posted By tonio100680
I really am a bioinformatics novice! I want a...

I really am a bioinformatics novice! I want a simple converter... It's panic. I'm harassed by biologists
Forum: Bioinformatics 06-07-2011, 10:16 PM
Replies: 14
Views: 10,885
Posted By tonio100680
Thank you for the help ! After converting my...

Thank you for the help !

After converting my files are formatted QSEQ. To use Novobarcode must convert them FASTQ. If so have you a simple solution?
Forum: Bioinformatics 05-30-2011, 05:00 AM
Replies: 14
Views: 10,885
Posted By tonio100680
Demultiplexing and CASAVA 1.7

Hello,
I am looking for young bioinformatics. I need tools to perform demultiplexing
tool (script) to sequences from the GAIIx before CASAVA (1.7). We do not use the index provided by Illumina....
Forum: Introductions 04-14-2011, 07:03 AM
Replies: 373
Views: 145,497
Posted By tonio100680
Hello, I am a biologist who has turned into a...

Hello,
I am a biologist who has turned into a bioinformatics engineer. I'll start working on a GAIIx Illumina in a French region ...
I have little contact and I hope through this forum to get...
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