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Search took 0.00 seconds. Search: Posts Made By: NikTuzov
Forum: Genomic Resequencing 06-21-2016, 12:29 PM
Replies: 1
Views: 3,839
Posted By NikTuzov
Variants inside and outside of target region - what's the difference?

Hello:

I am trying to understand whether there is some drastic difference between on-target and off-target reads. I assume that even if there is a true variant outside of target region, it is not...
Forum: Bioinformatics 01-26-2016, 08:17 AM
Replies: 0
Views: 830
Posted By NikTuzov
What is a Ti/Tv counterpart for indels?

Hello all:

Ti/Tv can be used for assessing the quality of SNV call set. Is there a statistic for indels that can be used for the same purpose?

Thanks,
Nik
Forum: Bioinformatics 09-08-2015, 09:04 AM
Replies: 1
Views: 1,416
Posted By NikTuzov
Using GATK's local realigner outside of GATK pipeline for variant calling

Hello all:

If I were to use GATK's local realigner outside of GATK pipeline, eg:

BWA -> GATK's Local Realigner -> SAMTools

then will I have any extra problems because I use non-GATK modules...
Forum: Bioinformatics 07-17-2015, 07:24 AM
Replies: 2
Views: 2,557
Posted By NikTuzov
Yes, you seem to be right as far as GATK is...

Yes, you seem to be right as far as GATK is concerned. Are there any other papers/software that implement some kind of normalization?
Forum: Bioinformatics 07-16-2015, 08:36 AM
Replies: 2
Views: 2,557
Posted By NikTuzov
Normalization by the library size during variant detection

Hello:

Suppose I have two libraries that do not have the same number of reads, but otherwise they are similar. During variant detection, more variants will be called in the larger library just...
Forum: Bioinformatics 08-18-2014, 11:58 AM
Replies: 2
Views: 2,106
Posted By NikTuzov
Thanks a lot. Nik

Thanks a lot.

Nik
Forum: Bioinformatics 08-13-2014, 02:47 PM
Replies: 2
Views: 2,106
Posted By NikTuzov
A question about TPM normalization

Hello:

Please tell me if I got it right. In the attached paper, the average read length, rl, is not necessary to know for computing TPM. It is sample-specific, but not gene-specific, and that is...
Forum: Bioinformatics 08-29-2013, 08:01 AM
Replies: 24
Views: 34,149
Posted By NikTuzov
Thanks. I take it the encoding of missing values...

Thanks. I take it the encoding of missing values depends on the sequencer and it cannot be changed downstream. Therefore, I don't see how some downstream tool can use 93 as a missing value when it is...
Forum: Bioinformatics 08-29-2013, 07:25 AM
Replies: 24
Views: 34,149
Posted By NikTuzov
Hi: I have a question about the so-called...

Hi:

I have a question about the so-called Sanger format where Q can be in [0;93] represented by [!-~]. Since this is the set of all visible ASCII characters, then it looks like there is no symbol...
Forum: RNA Sequencing 07-23-2013, 01:24 PM
Replies: 0
Views: 1,027
Posted By NikTuzov
Getting a certain quantitative metric from Cufflinks/Cuffdiff

Hello:

Could you please help me figure out how to get a certain quantitative metric from Cufflinks/Cuffdiff.

Suppose I want to stop at quantification without going for differential expression...
Forum: Bioinformatics 04-16-2013, 09:30 AM
Replies: 6
Views: 2,105
Posted By NikTuzov
Actually, I made a mistake. If Poisson is used in...

Actually, I made a mistake. If Poisson is used in Model 1, then the p-value can be obtained even without replication. The Poisson setup approximately corresponds to the raw counts being...
Forum: Bioinformatics 04-15-2013, 07:48 AM
Replies: 6
Views: 2,105
Posted By NikTuzov
this is all the more true for cancer and normal...

this is all the more true for cancer and normal samples, because here the variance for a gene can be completely different in both groups as well as compared to other genes...

-------------

How...
Forum: Bioinformatics 04-15-2013, 07:44 AM
Replies: 6
Views: 2,105
Posted By NikTuzov
Your test for model 2 is, afaIcs, more...

Your test for model 2 is, afaIcs, more susceptible to rejections for one gene when in fact other genes are differentially expressed (esp. if the latter take up a lot of reads).

-------------

In...
Forum: Bioinformatics 04-12-2013, 01:44 PM
Replies: 6
Views: 2,105
Posted By NikTuzov
One can also say that Model 2) contains more...

One can also say that Model 2) contains more information about the data: it is always possible to convert 2) into 1), but not the other way round. Why do they lose information on purpose?
Forum: Bioinformatics 04-12-2013, 09:29 AM
Replies: 6
Views: 2,105
Posted By NikTuzov
RNA-Seq, Differential Expression: a theoretical question of modeling methodology

Could you please help understand where I went wrong on the issue described below.

Suppose I am interested in detecting differential expression (DE) of a fixed transcript X between Tumor and Normal...
Forum: Bioinformatics 03-19-2013, 02:41 PM
Replies: 9
Views: 8,260
Posted By NikTuzov
Are you saying that the score is not available...

Are you saying that the score is not available unless I run tophat-fusion-post option? I hoped to find it in fusions.out produced by --fusion-search option.
Forum: Bioinformatics 03-18-2013, 07:37 AM
Replies: 9
Views: 8,260
Posted By NikTuzov
deFuse and TopHat-Fusion are used together here: ...

deFuse and TopHat-Fusion are used together here:

Transcriptome Profiling of the Cancer, Adjacent Non-
Tumor and Distant Normal Tissues from a Colorectal
Cancer Patient by Deep Sequencing
Yan’an...
Forum: Bioinformatics 03-15-2013, 02:41 PM
Replies: 9
Views: 8,260
Posted By NikTuzov
Hello: Could you please help me with a basic...

Hello:

Could you please help me with a basic question.

The documentation on this page:

http://tophat.cbcb.umd.edu/fusion_manual.html#output

says nothing about where to find the fusion...
Showing results 1 to 18 of 18

 


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