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Search: Posts Made By: CNVboy
Forum: Bioinformatics 05-15-2013, 02:51 PM
Replies: 1
Views: 1,708
Posted By CNVboy
Was the data for the ClinSeq SNP project obtained from patients or general population

SNP database from 1000G or NHLBI projects are based on general population, or presumably "healthy" people.

A long-time confusing question for me is, ClinSeq SNP project is based on just patients?...
Forum: Bioinformatics 03-17-2012, 04:22 PM
Replies: 12
Views: 4,468
Posted By CNVboy
Sounds interesting. Can you explain a little bit...

Sounds interesting. Can you explain a little bit more?
One problem for assembly is, what if say the deletion is heterozygous, which means there'll still be some reads mapping to the deleted parts....
Forum: Bioinformatics 03-17-2012, 01:17 PM
Replies: 2
Views: 5,902
Posted By CNVboy
unmapped vs soft-clipping

quite confused about this two terminology. I'm reading Pindel, the split-read algorithm. The author seems to make use of the information of "unmapped" reads. Also there are other split-read-based...
Forum: Bioinformatics 03-17-2012, 12:41 PM
Replies: 11
Views: 14,838
Posted By CNVboy
This may be a late answer. To my...

This may be a late answer.
To my understanding, you guys are confused about "-q opiton(quality trimming)" and " soft-clipped".

-q option is to trim those crappy ends of reads with very low...
Forum: Bioinformatics 03-17-2012, 10:06 AM
Replies: 12
Views: 4,468
Posted By CNVboy
Hi Kai, you are definitely right. Pindel is quite...

Hi Kai, you are definitely right. Pindel is quite special, which finds small indels while others cannot. So I usually never compare Pindel results with CNVnator/Breakdancer/VariationHunter. But...
Forum: Bioinformatics 03-09-2012, 07:11 AM
Replies: 12
Views: 4,468
Posted By CNVboy
General question: human CNV/Structural variants algorithms using next-gen data cannot

This is pretty much a general question in human CNV/Structural variants field (with next-gen data, NOT arrays).

As shown in 1000genome project, groups develop different algorithm-based approach to...
Forum: Bioinformatics 01-29-2012, 05:28 AM
Replies: 6
Views: 2,029
Posted By CNVboy
Have you solved your problem? thx

Have you solved your problem?
thx
Forum: Bioinformatics 11-27-2011, 04:52 PM
Replies: 1
Views: 1,725
Posted By CNVboy
BWA trim doesn’t work.

I tried to run BWA with trimming those low-quality bases around the end of read. And command is like:

/share/bin/bwa aln -t 7 -I -q 20 ****.txt.gz > ****.sai

Here -I is to convert Illumina...
Forum: Bioinformatics 11-19-2011, 03:39 PM
Replies: 1
Views: 2,566
Posted By CNVboy
Pindel problem

I downloaded the binary code of latest version of Pindel.
And then run the command like below;

./pindel_x86_64 -f /home/xxx/data/human_g1k_v37.fasta -i /home/xxx/scratch/S00005/config.txt -c ALL...
Forum: Bioinformatics 10-21-2011, 06:07 AM
Replies: 39
Views: 15,121
Posted By CNVboy
What do you mean by "cannot get into root". Have...

What do you mean by "cannot get into root". Have you downloaded ROOT package?
You'd better download the newest version of ROOT.(Old version may have bugs)
Then install CNVnator.

btw, ROOT is...
Forum: Bioinformatics 09-14-2011, 09:03 AM
Replies: 0
Views: 1,666
Posted By CNVboy
Variation-Hunter empty output

I don't know if anyone here has used Variation-Hunter.
I used the *.vh files generated from mrFAST as the input of Variation-Hunter.

But it seems I only get empty output.
15M...
Forum: Bioinformatics 07-07-2011, 12:15 PM
Replies: 0
Views: 2,225
Posted By CNVboy
CNVnator make histogram problem

I'm doing trio data analysis; so I merged those small root files into larger ones chromosome by chromosome. The merge process looks ok.

But when I tried to make histogram out of it, I got errors...
Forum: Bioinformatics 07-05-2011, 08:07 AM
Replies: 2
Views: 2,541
Posted By CNVboy
CNV core dump problem

HI I'm using CNVnator to do some CNV analysis but came across problems of core dump

Basically I first generated .root files from .bam files; then merged those small .root files into larger ones....
Forum: Bioinformatics 06-27-2011, 03:03 PM
Replies: 0
Views: 1,423
Posted By CNVboy
Save error report as text file in BWA

Hi I'm using SUN Grid Engine to submit BWA jobs, written by shell script like this:

#!/bin/bash

#$ -pe single 24
#$ -V
#$ -cwd
#$ -o $HOME/sge_jobs_output/sge_job.$JOB_ID.out -j y
#$ -S...
Forum: Bioinformatics 06-22-2011, 05:13 AM
Replies: 5
Views: 2,093
Posted By CNVboy
THanks everyone. I think the core question...

THanks everyone.

I think the core question is: how can we guarantee the quality of the generated .sai, .sam file? How do you know the programming at this step is complete? Just look at the size of...
Forum: Bioinformatics 06-21-2011, 03:13 PM
Replies: 5
Views: 2,093
Posted By CNVboy
About script to combine steps of BWA

For BWA, first do alignment (generate .sai), then sampe the paired-ends (generate .sam), then convert .sam to .bam. Now I'm going to write script to combine all these steps. ie, input is fastq, then...
Forum: Bioinformatics 06-16-2011, 06:33 PM
Replies: 1
Views: 2,071
Posted By CNVboy
Unhappy BWA weird thing

HI guys

I ran programs to generate .sam files, but find some weird things.
432M ERR001275_1.recal.fastq.gz
432M ERR001275_1.sai
434M ERR001275_2.recal.fastq.gz
437M ERR001275_2.sai
8.0K...
Forum: Bioinformatics 06-16-2011, 05:58 AM
Replies: 39
Views: 15,121
Posted By CNVboy
Thx Prakhar, Sorry for my delayed response....

Thx Prakhar,

Sorry for my delayed response. The problem of viewing has been solved. Yeah, you are right, use ssh -X and it works! thx~

I'm actually now trying larger-scale data on cluster, and...
Forum: Bioinformatics 06-15-2011, 11:56 AM
Replies: 1
Views: 2,528
Posted By CNVboy
Confused about .sai file size

Yesterday I ran hundreds, if not thousands of alignment of fastq files to human genome, so I have some findings. Just look at below:

1.3G SRR010942_2.recal.fastq.gz
259M SRR010942_2.sai...
Forum: Bioinformatics 06-14-2011, 04:40 PM
Replies: 5
Views: 3,251
Posted By CNVboy
Many many thanks Kennels!!! Yeah, I just...

Many many thanks Kennels!!!

Yeah, I just made the spreadsheet, actually with 800 fastq files. And the shell script works quite well!
btw, can you give any clue about writing Perl to finish such...
Forum: Bioinformatics 06-14-2011, 03:02 PM
Replies: 5
Views: 3,251
Posted By CNVboy
Run hundreds of BWA commands without waiting

Hi guys
I'm analyzing some high-coverage trio data. So Need to run BWA for hundreds of fastq.gz files. Obviously I should write some script to finish such task without waiting and typing in hundreds...
Forum: Bioinformatics 06-14-2011, 05:38 AM
Replies: 39
Views: 15,121
Posted By CNVboy
thx guys. I tried using ssh -X, but still...

thx guys.

I tried using ssh -X, but still doesn't work.

[xug@pem610-006 src]$ ./cnvnator -root NA18507.root -view 100
>chr12 11396601 11436500
>

I can see nothing except the new prompt.
Forum: Bioinformatics 06-13-2011, 07:54 PM
Replies: 39
Views: 15,121
Posted By CNVboy
yeah, I'm using ssh. I google ssh option,...

yeah, I'm using ssh.

I google ssh option, and -X seems to mean to enable X11 forwarding....But I'm still confused about how this has anything to do with my problem of...
Forum: Bioinformatics 06-13-2011, 02:35 PM
Replies: 39
Views: 15,121
Posted By CNVboy
Just now I tried the whole genome (no longer...

Just now I tried the whole genome (no longer specific to chr1): ./cnvnator -root NA18507. root -tree ***.bam

Then it pop out:
Out of bound coordinate 199501844 for chromosome 'chr3'.
Out of...
Forum: Bioinformatics 06-13-2011, 02:21 PM
Replies: 39
Views: 15,121
Posted By CNVboy
thx Michael. Now I've gone through the...

thx Michael.

Now I've gone through the whole steps of CNVnator and seems quite good. The only problem now is at the final step about visualizing the CNV. I enter a genomic region at the prompt...
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