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Forum: Bioinformatics 12-30-2013, 12:30 AM
Replies: 0
Views: 2,156
Posted By pirates.genome
Question visualization of CNV with genomic coordinates in R ggplot2 or ggbio

Hi all,

I came through a heatmap of CNVs from Illumina Genome Studio which has four samples (see attachment). On Y axis they have genomic coordinates and on X axis the samples. Red denotes...
Forum: Bioinformatics 07-28-2013, 07:06 PM
Replies: 2
Views: 1,306
Posted By pirates.genome
Genomic data plotting/visualization

Hi all,

I was going through some gneomic articles and found several similar figures with similar layout/format. Is there any software or R-module for ploting such multi-dimentional figures (number...
Forum: Bioinformatics 03-21-2013, 12:43 PM
Replies: 3
Views: 1,011
Posted By pirates.genome
Thanx GenoMax for quick reply. wordCluster...

Thanx GenoMax for quick reply.

wordCluster is doing what I already did. I have identified regulatory elements from my genome sequence. Now I want to find out the occurrence of such regulatory...
Forum: Bioinformatics 03-21-2013, 06:29 AM
Replies: 3
Views: 1,011
Posted By pirates.genome
Question random occurrence of regulatory element in genome

Hi all,

I have detected some regulatory sequences of 13 mer from genome sequencing study. The 13-mer has a consensus sequence of GNACANNNTGTNC. How can I calculate occurrence of this 13-mer in the...
Forum: Bioinformatics 08-18-2012, 11:07 AM
Replies: 5
Views: 8,703
Posted By pirates.genome
Smile Hi Richard Finney, Thank you for very helpful...

Hi Richard Finney,
Thank you for very helpful code. First code worked good for me.
:)
Forum: Bioinformatics 08-16-2012, 05:38 AM
Replies: 5
Views: 8,703
Posted By pirates.genome
Thnx colindaven, I looked into samtools view...

Thnx colindaven,

I looked into samtools view -L option but that is not what I am looking for.

Let me explain the problem,
I have targeted DNA sequencing data from Illumina. After aligning to...
Forum: Bioinformatics 08-14-2012, 06:21 AM
Replies: 5
Views: 8,703
Posted By pirates.genome
Question Extract aligned sequence coordinates from SAM or BAM file

Hi,
I have a Illumina sequence reads which I mapped to HG19 using BWA. Resulting BAM file is indexed and sorted. Now what I want is to identify the region of alignment. Let me give an example, on...
Forum: Bioinformatics 06-19-2012, 01:21 AM
Replies: 2
Views: 2,983
Posted By pirates.genome
Thats what I was looking for!

Thank you Dario for the reply. I was looking for the same.
Forum: Bioinformatics 06-18-2012, 12:36 AM
Replies: 2
Views: 2,983
Posted By pirates.genome
Question Filter paired & mapped reads from SAM/BAM file

Hi,
I have SAM/BAM files of paired end Illumina sequencing obtained by BWA.

I want to filter out all reads having "proper pair" and both the reads of pair aligned to references. How can I filter...
Forum: Bioinformatics 03-08-2012, 12:27 PM
Replies: 2
Views: 1,067
Posted By pirates.genome
Thank you swbarnes2 for explaining why only first...

Thank you swbarnes2 for explaining why only first base is not so good as variant rather true SNP should be covered by many different reads starting at different positions.

It is targeted...
Forum: Bioinformatics 03-08-2012, 08:47 AM
Replies: 2
Views: 1,067
Posted By pirates.genome
Question First base of reads SNP or false result?

Hi,
I am using 5 samples pooled DNA Targeted sequencing data (Illumina FASTQ) and using BWA - GATK for mapping and variant calling. In variant calls (vcf files), I find that at aparticular position...
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