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Search: Posts Made By: lyz1030
Forum: Bioinformatics 12-04-2013, 08:22 PM
Replies: 0
Views: 1,397
Posted By lyz1030
Where can I download Venter Genome's structural variants?

Hi,

Can anyone tell me where can I download Venter Genome's structural variants (hg19 or build 37)?

Thanks,

Eric
Forum: Bioinformatics 02-06-2013, 07:38 AM
Replies: 1
Views: 1,240
Posted By lyz1030
velvet in heterozygous site

Hi,

I want to use velvet to do de novo assembly on a particular region (in a bam file) and this region contain a heterozygous site. I intuitively think it should generate two contigs in this...
Forum: Bioinformatics 11-05-2012, 05:30 PM
Replies: 1
Views: 1,814
Posted By lyz1030
what do you mean average variant location of...

what do you mean average variant location of reads? the average distance to 5' end of the read?
Forum: Bioinformatics 11-05-2012, 05:28 PM
Replies: 1
Views: 2,310
Posted By lyz1030
I want to know if bedtools can convet vcf file to...

I want to know if bedtools can convet vcf file to bed file ?
Forum: Bioinformatics 11-05-2012, 05:26 PM
Replies: 0
Views: 1,346
Posted By lyz1030
Annotate vcf file with RepeatMasker

Can anyone tell me how to annotate vcf file with UCSC RepeatMasker track?

thanks
Forum: Bioinformatics 10-21-2012, 01:30 PM
Replies: 1
Views: 2,179
Posted By lyz1030
extra high coverage regions in exome sequencing data

Hi everyone,

What reasons are the extra high coverage regions in exome sequencing data caused by? I want to know if can affect variant calling. What effect can it bring, false positive or false...
Forum: Bioinformatics 09-20-2012, 12:31 PM
Replies: 2
Views: 1,239
Posted By lyz1030
sequencing reads simulation

Hi,



Can anyone explain the results of wgsim of me? What does the character 'R', 'M', 'Y' stands for in the third column? What is the meaning of the second column? In addition, if I have two...
Forum: Illumina/Solexa 09-20-2012, 12:27 PM
Replies: 1
Views: 1,439
Posted By lyz1030
sequencing reads simulation

Hi,



Can anyone explain the results of wgsim of me? What does the character 'R', 'M', 'Y' stands for in the third column? What is the meaning of the second column? In addition, if I have two...
Forum: Bioinformatics 09-20-2012, 09:39 AM
Replies: 6
Views: 4,948
Posted By lyz1030
can anyone tell me how wgsim simulate variants...

can anyone tell me how wgsim simulate variants (the position can be specified ) or we can get the variant position. The objective is to evaluate the false negative rate of variant calling softwares.
Forum: Bioinformatics 09-14-2012, 11:25 AM
Replies: 3
Views: 1,893
Posted By lyz1030
I can's find enough trio data except two trios of...

I can's find enough trio data except two trios of 1000 Genomes Project.
Forum: Bioinformatics 09-11-2012, 04:16 PM
Replies: 3
Views: 1,893
Posted By lyz1030
Trio sequencing data simulation

Hi,
Can anyone give me some suggestions how to simulate a trio's sequencing data? I think the most important part is how to using parents's genome to simulate the offspring's genome according to the...
Forum: Bioinformatics 07-12-2012, 05:36 AM
Replies: 2
Views: 1,499
Posted By lyz1030
I use the bwa results as the input, so the input...

I use the bwa results as the input, so the input reads is refered to the reads from the bam file. For this kinds of reads (reverse strand), I am not sure which end is the 3' end. I don't know why the...
Forum: Bioinformatics 07-12-2012, 05:17 AM
Replies: 2
Views: 1,499
Posted By lyz1030
calculate a base's distance to the read's 3' end

Hi,



Can anyone tell me how to calculate a base's distance to 3' end respectively for the forward and reverse strand read. I want to konw if the following formula is correct?



1)for...
Forum: Bioinformatics 07-11-2012, 10:03 AM
Replies: 1
Views: 1,168
Posted By lyz1030
Distance to 3 end

Can anyone tell me how to find a variant's distance to 3 end? Which file or database can I use to annotate my variant file.
Forum: Bioinformatics 07-09-2012, 07:38 AM
Replies: 1
Views: 5,062
Posted By lyz1030
strand bias P-value

Can anyone tell me how to calculate the strand bias P-value?
Forum: Bioinformatics 05-08-2012, 01:18 PM
Replies: 1
Views: 1,330
Posted By lyz1030
N in the reference genome

If a base in the reference genome is 'N', how can we decide if this site is a variant or not?
Forum: Bioinformatics 05-02-2012, 07:32 AM
Replies: 0
Views: 1,171
Posted By lyz1030
Picard's SamLocusIterator

Hi,



Can anyone tell me how to find 'ref allele' and 'indel' in a position using SamLocusIterator?



Thanks
Forum: Bioinformatics 05-01-2012, 01:26 PM
Replies: 0
Views: 1,186
Posted By lyz1030
ordering of genotypes for the likelihoods

Hi ,

As to the GL field (ordering of genotypes for the likelihoods, F(j/k) = (k*(k+1)/2)+j) of vcf spec 4.1...
Forum: Bioinformatics 04-30-2012, 06:02 PM
Replies: 8
Views: 14,324
Posted By lyz1030
Compare VCF Files

Can anyone tell me how to compare the vcf files to find the differences of two or more? Use Existing tools or souce code?
Forum: Bioinformatics 04-20-2012, 11:46 AM
Replies: 0
Views: 1,781
Posted By lyz1030
Using Java to process BCF (binary VCF)

Hi,
Can someone tell me if there is the source code to read or write BCF format data (samtools output) in Picard? or in some other open source tools?
Thanks!
Forum: Bioinformatics 04-18-2012, 09:24 PM
Replies: 5
Views: 2,013
Posted By lyz1030
For your first question, I merely want to get...

For your first question, I merely want to get records in every locus simultaneously, not in any other order.
Forum: Bioinformatics 04-18-2012, 09:21 PM
Replies: 5
Views: 2,013
Posted By lyz1030
Nils, thanks a lot for you suggestions. For...

Nils, thanks a lot for you suggestions. For example, I have two different bam files (from two samples, like normal and tumor, more than 2 bam files are also OK) and these two files are ordered by...
Forum: Bioinformatics 04-18-2012, 04:54 PM
Replies: 5
Views: 2,013
Posted By lyz1030
I try to use multiple iterators...

I try to use multiple iterators (SamLocusIterator) to solve this problem. Howerver, it is very difficult to control the iterator order. I want to process the pileups from mutiple sam file when...
Forum: Bioinformatics 04-18-2012, 02:15 PM
Replies: 5
Views: 2,013
Posted By lyz1030
Picard's SamLocusIterator

Hi,

I want to use Picard to traverse mutiple sam file from different samples simultaneously. The information on every locus (from all the bam files) is useful to me. Now, I find 'SamLocusIterator'...
Forum: Bioinformatics 04-13-2012, 01:37 PM
Replies: 2
Views: 1,646
Posted By lyz1030
About Picard and SAM-JDK

Hi,

I have a question about SAM-JDK. In the class 'net.sf.samtools.SAMRecord', what is the meaning of the method getReadPairedFlag() and getProperPairFlag(). If getReadPairedFlag() returns ture...
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