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Forum: Bioinformatics 08-29-2016, 11:09 AM
Replies: 7
Views: 2,032
Posted By kjaja
Any help will greatly be appreciated.

Any help will greatly be appreciated.
Forum: Bioinformatics 08-20-2016, 01:10 PM
Replies: 7
Views: 2,032
Posted By kjaja
Thanks Michael for your help I have one more...

Thanks Michael for your help
I have one more question , do I need to perform a between-sample normalization before using the following design ?

ddsTC <- DESeqDataSet(dds, ~ time)
ddsTC <-...
Forum: Bioinformatics 07-13-2015, 10:56 AM
Replies: 7
Views: 2,032
Posted By kjaja
question related to analysis using DESeq2

Hi,

when using the following design to test for differentila expression

ddsTC <- DESeqDataSet(dds, ~ time)
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ 1)
resTC <- results(ddsTC)

How to...
Forum: Bioinformatics 02-09-2015, 10:22 AM
Replies: 7
Views: 2,032
Posted By kjaja
Thanks Michael , To follow up on my original...

Thanks Michael ,

To follow up on my original post, I am trying to compare the results between DESeq and DESeq 2 and found the output was very different (correlation=0.59), is that expected? I have...
Forum: Bioinformatics 02-05-2015, 01:05 PM
Replies: 7
Views: 2,032
Posted By kjaja
Question related to analysis using DESeq2

Hi All,

I have expression data for a mutant where a drug is injected over time with increasing dosage (no replicates and no drug was injected at time 0). I would like to identify genes that change...
Forum: Bioinformatics 12-29-2014, 12:54 PM
Replies: 12
Views: 8,284
Posted By kjaja
DESeq2

I read the example of a basic analysis of a time-series experiment at the bottom of this workflow:
http://bioconductor.org/help/workflows/rnaseqGene/

the fission data had replicates for both...
Forum: Bioinformatics 07-30-2014, 08:49 AM
Replies: 3
Views: 1,390
Posted By kjaja
analyzing RNA seq

Hi All,

I have RNA sequencing data (expression data) for a control sample and cases (with disease) and at multiple time points but no replicates of. any ideas on how to analyze this type of data? ...
Forum: Bioinformatics 04-16-2014, 11:45 AM
Replies: 2
Views: 1,660
Posted By kjaja
Online Variant Annotation Tool

Hi All,

Does anyone recommend an online variant annotation tool that also makes functional predictions? it would be nice if the tool also provides biological pathways if possible
Forum: Bioinformatics 04-13-2014, 05:25 PM
Replies: 4
Views: 1,072
Posted By kjaja
thanks, since my data is RNA seq, can I use STEM...

thanks, since my data is RNA seq, can I use STEM analyze it? it seems that it is designed for microarray data.
Forum: Bioinformatics 04-13-2014, 03:06 PM
Replies: 4
Views: 1,072
Posted By kjaja
analyzing RNA seq

Hi All,

I have RNA sequencing data (expression data) for a control sample and case1 (with disease) and case 2(with a more severe disease)at multiple time points. i.e the expression of each gene is...
Forum: Bioinformatics 07-02-2013, 05:24 AM
Replies: 1
Views: 1,325
Posted By kjaja
question on filtering variants

Hi,

I am working on identifying variants in affected individuals the we exome sequenced. Going through the variants after filtering out variants in the 1000 Genomes project, dbSNP and ESP6500, I...
Forum: Bioinformatics 04-09-2013, 09:55 AM
Replies: 11
Views: 3,174
Posted By kjaja
I have tried using vcf-contrast in vcf tools...

I have tried using vcf-contrast in vcf tools using the following command

vcftools_0.1.10/perl/vcf-contrast +sample1,sample2 -sample3 -n allAllsamples.vcf > insample1or2NOTsample3.vcf

where I...
Forum: Bioinformatics 04-08-2013, 03:00 PM
Replies: 11
Views: 3,174
Posted By kjaja
Was wondering if this can be done using GATK?

Was wondering if this can be done using GATK?
Forum: Bioinformatics 04-06-2013, 06:59 AM
Replies: 11
Views: 3,174
Posted By kjaja
I have tried the vcf tool vcf-contrast from the...

I have tried the vcf tool vcf-contrast from the following link http://vcftools.sourceforge.net/perl...l#vcf-contrast
but i am getting the following warning

Argument "." isn't numeric in numeric...
Forum: Bioinformatics 04-04-2013, 12:19 PM
Replies: 11
Views: 3,174
Posted By kjaja
variant filtering

Hi All,

I have cases and controls the were exomed sequenced and used GATK to call the variants in all the cases and controls combined. This generated a single vcf file with all the variants. I...
Forum: Bioinformatics 03-21-2013, 12:37 PM
Replies: 10
Views: 5,749
Posted By kjaja
gender check using sequencing data

Hi All,

I have exome sequencing data from siblings and would like to confirm their gender and relationship using genetics to make sure they are in fact siblings. I also want to confirm that the...
Forum: Bioinformatics 03-19-2013, 10:39 AM
Replies: 0
Views: 1,246
Posted By kjaja
calling variants using GATK

Hi All,

I was wondering about the difference between the Haplotype Caller and the Unified Genotype caller within GTAK for calling variants from exome sequencing. I know that the Haplotype Caller...
Forum: Bioinformatics 03-18-2013, 03:42 PM
Replies: 1
Views: 1,182
Posted By kjaja
Question related to choosing GATK parameter for variant calling

I am looking to call my samples that were exome sequenced using UnifiedGenotyper program within GATK. An example of a generic command is given in the following link under “Example generic command for...
Forum: Bioinformatics 02-21-2013, 06:04 AM
Replies: 8
Views: 3,592
Posted By kjaja
THANKS! but there seem to be syntax error in the...

THANKS! but there seem to be syntax error in the last code awk command? I am not sure how to fix it?
Forum: Bioinformatics 02-20-2013, 03:39 PM
Replies: 8
Views: 3,592
Posted By kjaja
Hi Below is a sample output for the coverage...

Hi

Below is a sample output for the coverage file from bedtools, the coverage ranges from 0 to 8 for the same region (column 5), so I want to see what percentage of the exome was covered by at...
Forum: Bioinformatics 02-20-2013, 10:48 AM
Replies: 8
Views: 3,592
Posted By kjaja
coverage calculation for exome data

Hi,

I am looking to calculate what percentage of all target positions achieved a coverage of at least 50x? can this be done?


Appreciate your help
Forum: Bioinformatics 12-15-2012, 05:30 PM
Replies: 0
Views: 1,861
Posted By kjaja
power calculation for exome seq

Hi All,

I am designing an experiment to perform exome sequencing on 20 affected with their parents (trios) for detecting de novo mutations. I would like to perform a power calculation to see if I...
Forum: Bioinformatics 06-08-2012, 09:17 AM
Replies: 3
Views: 1,595
Posted By kjaja
when filtering out variants in the 1000 genomes,...

when filtering out variants in the 1000 genomes, I am left with variants that were not filterd out becuase the region was not well covered in the 1000 genomes.
Forum: Bioinformatics 06-07-2012, 08:37 PM
Replies: 3
Views: 1,595
Posted By kjaja
how to get coverage information from the 1000 genomes data

Hi All,

What is the best way to check if a variant at a specific location is well covered in the 1000 genomes. The way that I am pulling this information is by slicing the bam files and viewing...
Forum: Bioinformatics 05-31-2012, 04:46 PM
Replies: 3
Views: 1,562
Posted By kjaja
calculating the coverage over a gene

Hi,

I am interested in knowing the mean coverage for a specific region (for example a gene). Is this possible to calculate? If so how ?

Thanks for your help…
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