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Search: Posts Made By: yuhao
Forum: Bioinformatics 08-15-2012, 09:42 AM
Replies: 4
Views: 3,006
Posted By yuhao
I am not able to open the link, could you send...

I am not able to open the link, could you send the article to me in : hhhyyyccc@gmail.com
Forum: Bioinformatics 08-13-2012, 07:10 AM
Replies: 1
Views: 931
Posted By yuhao
effect to variation detection if the reads are not distributed uniformly

What happen if the sequenced reads don't distribute uniformly across the genome? What is the resulting effect for variation detection? Is there any qualitative research on this?I see many papers...
Forum: Bioinformatics 08-11-2012, 10:59 AM
Replies: 4
Views: 3,006
Posted By yuhao
Hi, stefanoberri, I am not able to access the...

Hi, stefanoberri, I am not able to access the paper for CNAnorm, could you mind to send me the paper in mailbox: hhhyyyccc@gmail.com? I appreciate it !
Forum: Bioinformatics 08-11-2012, 08:21 AM
Replies: 2
Views: 1,267
Posted By yuhao
Forum: Bioinformatics 08-10-2012, 05:29 AM
Replies: 2
Views: 1,196
Posted By yuhao
Yes, I mean the length of the CNV. I am intersted...

Yes, I mean the length of the CNV. I am intersted in tumor cells
Forum: Bioinformatics 08-09-2012, 10:00 PM
Replies: 2
Views: 1,196
Posted By yuhao
tumor cell variation size

Is there any statistics about the tumor cell CNV size?
Forum: Bioinformatics 08-09-2012, 01:58 PM
Replies: 4
Views: 3,006
Posted By yuhao
Recommendation for CNV detection software in Illumina WGS data for cancer cells

Can anyone recommend some reliable software for CNV detection in cancer cells for Illumina WGS data?
Forum: Bioinformatics 08-09-2012, 06:22 AM
Replies: 0
Views: 1,268
Posted By yuhao
Does the read depth distribution(not read depth) matters

In CNV detection, many papers indicates read depth, but does the distribution of read depth matters? Is an extremely uneven read depth acceptable for CNV analysis?Will it lead accurate CNV calls?I...
Forum: Literature Watch 08-09-2012, 04:13 AM
Replies: 77
Views: 52,641
Posted By yuhao
Hi, valeu, I am currently have two cancer...

Hi, valeu,

I am currently have two cancer cells datas(the same cancer) from human, the coverage depth are about 33,39, with a depth statistics for each base. In this case, what is the best...
Forum: Bioinformatics 08-08-2012, 03:37 AM
Replies: 1
Views: 1,190
Posted By yuhao
normalized_RD signal is very large in CNVnator

I have a question, I have very large values for this
normalized_RD, likes 4.275*e^12 level (and the size of the CNV is
about e^6 level), is there anything wrong because of this? And does...
Forum: Bioinformatics 08-07-2012, 09:46 AM
Replies: 3
Views: 1,316
Posted By yuhao
hi, thank krobison! I still don't understand...

hi, thank krobison!
I still don't understand some points here. so choose all the SNP detected and labelled 1, 2, ...., so then we construct a hidden markov model with transition probability and...
Forum: Bioinformatics 08-07-2012, 01:46 AM
Replies: 3
Views: 1,316
Posted By yuhao
What does CNV has anything to do with SNP

In SNP genotyping array data, we use the singal intensity at each SNP to infer CNV by using Hidden Markov Model, what does CNV region has anything to do with SNP detected?I am so confused about this!...
Forum: Bioinformatics 08-06-2012, 08:39 PM
Replies: 0
Views: 985
Posted By yuhao
about hidden markov model

I am currently trying to understand the hidden markov model in the detection of CNV for SNP genotyping array data. But I am confused totally. I understand fully HMM model, but i even dont' understand...
Forum: Literature Watch 08-05-2012, 07:57 PM
Replies: 77
Views: 52,641
Posted By yuhao
I am very appreciated for your patient help! I...

I am very appreciated for your patient help! I have some other questions to see if I can get your help:

The output intervals have some overlaps, e.x., 58000, 8387999, 3 gain, 8386000, 9404999...
Forum: Literature Watch 08-03-2012, 06:14 AM
Replies: 77
Views: 52,641
Posted By yuhao
May I ask a question, what does the "ratio" mean...

May I ask a question, what does the "ratio" mean in FREEC? Thanks!
Forum: Literature Watch 08-02-2012, 11:40 PM
Replies: 77
Views: 52,641
Posted By yuhao
Thank you for your help! I meet another question:...

Thank you for your help! I meet another question: I want to plot the graph using makeGraph.R , when I run, it shows:

null device
1
Error in if (type.convert(args[6])) { :
missing...
Forum: Literature Watch 08-01-2012, 12:45 AM
Replies: 77
Views: 52,641
Posted By yuhao
a unusual problem in FREEC

I meet an unusual problem when I run FREEC. If I provide a mateCopyNumberFile, and then qsub, it will run sucessfully, but in fact I normally don't have mateCopyNumberFile, but if I don't provide it,...
Forum: Bioinformatics 07-31-2012, 04:19 AM
Replies: 0
Views: 1,110
Posted By yuhao
the output format of CNVnator

What's the fourth column in the output file of CNVnator? It seems it is not the normalized RD. And we have 9 columns totally, but in README it has only 6 columns totally.
Forum: Bioinformatics 07-23-2012, 02:09 AM
Replies: 0
Views: 846
Posted By yuhao
What's genotyping SNP data

Some software require the input file is genotyping SNP data, what does that mean? What's the difference between this and WGS data?
Forum: Bioinformatics 07-13-2012, 11:07 PM
Replies: 0
Views: 1,382
Posted By yuhao
what is the fourth column in the output file of CNVnator

what is the fourth column in the output file of CNVnator?It looks like it is not the normalized RD signal as shown in the README file.
Forum: Bioinformatics 07-13-2012, 10:41 PM
Replies: 0
Views: 935
Posted By yuhao
the RD signal in CNVnator is very small

Is it normal that the average RD signal is very small: 9.94189e-08+-0.624659?
Forum: Bioinformatics 07-12-2012, 07:42 AM
Replies: 1
Views: 1,387
Posted By yuhao
A problem in CNVnator

When I do the histogram in CNVnator I find that it shows on the screen:

maximum buffer size exceed

what is the problem here? Thank you for help!
Forum: Bioinformatics 07-12-2012, 07:17 AM
Replies: 0
Views: 1,271
Posted By yuhao
Help! a problem in CNVnator

When I do partition step, it shows:

Abnormal range (101, 120) (like this)

What does this mean? Anything wrong in the last steps?
Forum: Bioinformatics 07-12-2012, 06:53 AM
Replies: 0
Views: 1,262
Posted By yuhao
Why "zero values of GC correction" appears when doing CNVnator

When I do the thire step, i.e.,making statistics, it shows:

bin 1 with center 1.49052e+07 is not corrected
zero values of GC average

what does this mean? Is there anything wrong?
Forum: Bioinformatics 07-12-2012, 05:53 AM
Replies: 1
Views: 1,647
Posted By yuhao
A problem in the steps in CNVnator

For the second step in running CNVnator, I see from the README that:

Files with chromosome sequences are required and should reside in running directory or directory specified by -d option. Files...
Showing results 1 to 25 of 33

 


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