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Search: Posts Made By: casim
Forum: UK - Cambridge 04-18-2013, 12:42 PM
Replies: 0
Views: 2,560
Posted By casim
CASIM: Assembly of transcriptomes

What is the best program for de novo transcriptome assembly from short reads?

Trinity, Oases or other?
Forum: UK - Cambridge 04-18-2013, 12:41 PM
Replies: 1
Views: 3,131
Posted By casim
CASIM: Assembly Using Synteny information

Is there a program that allows you to use the genome sequences of closely related species to inform the assembly a the genome of a new species, while allowing for a potentially significant loss of...
Forum: UK - Cambridge 04-18-2013, 12:41 PM
Replies: 4
Views: 4,146
Posted By casim
CASIM: Assembly Gap Closure

What are the best methods/programs for attempting to close gaps between scaffolds after a de novo assembly has resulted in a large number of scaffolds (before resorting to further sequencing)?
Forum: UK - Cambridge 04-18-2013, 12:40 PM
Replies: 2
Views: 4,006
Posted By casim
CASIM: Assembly Metrics for Assembly quality

What are the best metrics for assessing assembly quality for a de novo genome assembly in a species with no sequenced closely related organisms?
Forum: UK - Cambridge 04-18-2013, 12:39 PM
Replies: 0
Views: 2,495
Posted By casim
CASIM: Alignment Allele specific aligners

Is anyone using aligners that cope with haplotypes?

i.e. assemblies like human and mouse that do not have a single path through the genome
Forum: UK - Cambridge 04-18-2013, 12:38 PM
Replies: 0
Views: 2,760
Posted By casim
CASIM: Variants Detection via assembly

To what extent can de novo assembly replace current SV detection approaches (such us Pindel, Delly or CNVnator) in the detection of structural variants?
Forum: UK - Cambridge 04-18-2013, 12:37 PM
Replies: 0
Views: 2,537
Posted By casim
CASIM: Variants, Detecting Aneuploidy

Whatís the best way of detecting aneuploidy in a whole genome data set?

Is read depth all that there is? Can we detect and use alterations in chromosomal SNP rates?

Any better approach?
Forum: UK - Cambridge 04-18-2013, 12:35 PM
Replies: 0
Views: 2,703
Posted By casim
CASIM: Variants Dealing with continual addition of data

Given that it is more powerful to call genomic variants from multiple samples simultaneously than on a sample-by-sample basis, how would you deal with a situation in which samples are added...
Forum: UK - Cambridge 04-18-2013, 12:33 PM
Replies: 0
Views: 2,526
Posted By casim
CASIM: RNA-Seq Variants Eliminating mapping bias

What steps have others taken to eliminate mapping bias favoring the reference allele when measuring allele specific expression from RNA-seq data?
Forum: UK - Cambridge 04-18-2013, 12:32 PM
Replies: 0
Views: 2,590
Posted By casim
CASIM: Variants Making use of array genotype data

If genotype data is available for the same individuals, at what stage would the data be most useful?

Should it be added at calling or VQSR (Variant Quality Score Recalibration) stage as a set of...
Forum: UK - Cambridge 04-18-2013, 12:31 PM
Replies: 0
Views: 2,569
Posted By casim
CASIM: Variants, Experimental Validation

What experimental validation should be done for computationally detected variants in genomic data?

What are the common practices?
Forum: UK - Cambridge 04-18-2013, 12:30 PM
Replies: 0
Views: 2,639
Posted By casim
CASIM: Variants Picking the best software

How can I decide what software is the "best" at calling SNP and indels, or should I take a consensus of various different tools?

Whatís the best program / approach for detecting Ďsmallí insertions...
Forum: UK - Cambridge 04-18-2013, 12:29 PM
Replies: 0
Views: 2,760
Posted By casim
CASIM: Variants, Filtering SNP Calls

Iím interested in filtering of SNP calls, which ones are real SNPs and which ones are artifacts?

What current methods would people recommend for calling variants & genotypes
Forum: UK - Cambridge 04-18-2013, 12:27 PM
Replies: 0
Views: 2,863
Posted By casim
CASIM: ChIP-Seq of Repetitive Regions

I am particularly interested in analysing repetitive sequences in the genome - ChIP-Seq of histone modifications that are associated with simple repeats or interspersed retroelements for example....
Forum: UK - Cambridge 04-18-2013, 12:26 PM
Replies: 1
Views: 2,979
Posted By casim
CASIM: ChIP-Seq of broad peaks

Which is the best program to compute differential histone modifications that cover broad domains like H3K9me2, and how would one consider the inputs for all samples.
Forum: UK - Cambridge 04-18-2013, 12:25 PM
Replies: 1
Views: 2,727
Posted By casim
Related Question: One way to compare binding...

Related Question:

One way to compare binding sites in multiple experiments is to generate a correlation matrix of all regions in all samples.* Are there other methods available?
Forum: UK - Cambridge 04-18-2013, 12:24 PM
Replies: 5
Views: 5,610
Posted By casim
Related Question: Which is the best method...

Related Question:

Which is the best method to use when quantitatively comparing different experiments of varying sequencing depths?
Forum: UK - Cambridge 04-18-2013, 12:24 PM
Replies: 5
Views: 5,610
Posted By casim
Related Question: What is the best way to...

Related Question:

What is the best way to normalize ChIP-seq data, particularly when working with multiple biological replicates and controls that may have differing numbers of sequenced tags?
Forum: UK - Cambridge 04-18-2013, 12:23 PM
Replies: 1
Views: 2,727
Posted By casim
CASIM: ChIP Seq Visualisation

ChIP-seq data visualization (not genome browser) is quite simple with one or two samples.* Most frequently used examples are venn diagrams.* What other options are available for displaying data...
Forum: UK - Cambridge 04-18-2013, 12:22 PM
Replies: 5
Views: 5,610
Posted By casim
CASIM: ChIP-Seq Normalisation

I would be interested in discussing normalization strategies for ChIP-seq data across (a large number of) samples. More specifically, how to account for library clonality artifacts, differences in IP...
Forum: UK - Cambridge 04-18-2013, 12:21 PM
Replies: 0
Views: 2,732
Posted By casim
CASIM: ChIP-Seq QC

What QC measures and tools are being used?

Read/mapping quality
Sequencing bias
Duplication rates
Cross-correlation
S/N
Forum: UK - Cambridge 04-18-2013, 12:20 PM
Replies: 0
Views: 2,766
Posted By casim
CASIM: ChIP-Seq Replicates

When designing a ChIP-Seq experiment. How many replicates should I be considering?

I would like to know if there are any specific methods or general strategies to estimate a-priori the variability...
Forum: UK - Cambridge 04-18-2013, 12:17 PM
Replies: 0
Views: 2,719
Posted By casim
CASIM: Single Cell RNA-Seq

I would like to bring up a topic of single cell RNA sequencing and how it compares to sequencing of RNA extracted from population of cells as well as single cell qPCR
Forum: UK - Cambridge 04-18-2013, 12:17 PM
Replies: 1
Views: 3,392
Posted By casim
CASIM: RNA-Seq Power Analysis

Is anyone developing, or has anyone applied, statistical approaches determining the power to detect differentially expressed genes in an RNA-seq experiment, leading to an estimate of the sample size...
Forum: UK - Cambridge 04-18-2013, 12:15 PM
Replies: 0
Views: 2,655
Posted By casim
CASIM: RNA-Seq Factors in experimental design

Which of these factors is important in RNA-Seq analysis

global vs nuclear RNA
strand-specific vs not
mapped to known transcripts only vs de novo transcript calls
alternative splicing...
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