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Search: Posts Made By: yl01
Forum: Bioinformatics 10-30-2014, 09:45 AM
Replies: 4
Views: 2,057
Posted By yl01
Thanks for the answers. I read a little more and...

Thanks for the answers. I read a little more and seem to have the answer to my question. Without both the -G and -g options when running cufflinks, cufflinks will run using the riginal cufflinks...
Forum: Bioinformatics 10-28-2014, 03:52 AM
Replies: 4
Views: 2,057
Posted By yl01
Running cufflinks without the -G or the -g option

Hi,

I am analyzing an RNA-seq dataset using tophat and cufflinks. Mostly I followed the procedures described in the Nature Protocol paper (http://www.ncbi.nlm.nih.gov/pubmed/22383036). According...
Forum: General 01-27-2014, 01:07 PM
Replies: 11
Views: 16,067
Posted By yl01
Igvtools (which is a command line tools...

Igvtools (which is a command line tools associated with IGV) count can do this task easily. It produces a text file in wig format. However it may not easy to open it in Excel as desired.
Forum: General 01-27-2014, 12:56 PM
Replies: 3
Views: 5,973
Posted By yl01
The advice we got from Agilent support people is...

The advice we got from Agilent support people is that for Haloplex data it is important not to remove PCR duplicates. Haloplex data sets are expected to produce a lot of reads with exact same start /...
Forum: Bioinformatics 11-28-2013, 04:17 AM
Replies: 9
Views: 6,741
Posted By yl01
Even if you have good internet connection,...

Even if you have good internet connection, Plink's annotation function will not work. That function is relying on an external database and it has been not woking for at least two years.
Forum: Bioinformatics 10-25-2013, 07:15 PM
Replies: 3
Views: 2,621
Posted By yl01
It looks like the vcftools you are using is of...

It looks like the vcftools you are using is of version 0.1.4a. So the first thing i would try is to install the updated version, which is 0.1.11.
Forum: Bioinformatics 09-27-2013, 05:53 AM
Replies: 0
Views: 1,226
Posted By yl01
Invalid VCF files from Lifescope - allele "-"

I found some problematic VCF files created by Lifescope software. The sequencing was done on Solid 5500. These VCFs cannot be merged with other VCF files. The variants in these files are all indels....
Forum: Bioinformatics 09-26-2013, 04:52 AM
Replies: 1
Views: 3,649
Posted By yl01
Anyone has an idea?

Anyone has an idea?
Forum: Bioinformatics 09-20-2013, 02:08 AM
Replies: 1
Views: 3,649
Posted By yl01
het/hom ratio of exome samples

We have sequenced whole exomes of a family with monogenic disease. The sequencing was done on Solid 5500 as single-end and data processed by Lifescope. We have got different QC metrics for the...
Forum: Bioinformatics 04-18-2013, 06:48 AM
Replies: 6
Views: 2,045
Posted By yl01
Thank you nexgengirl and Bukowski!

Thank you nexgengirl and Bukowski!
Forum: Bioinformatics 04-16-2013, 01:33 PM
Replies: 6
Views: 2,045
Posted By yl01
Thank you nexgengirl! I know it was using Agilent...

Thank you nexgengirl! I know it was using Agilent HaloPlex technology. So I think it is hybridization based. Right?
Forum: Bioinformatics 04-16-2013, 07:25 AM
Replies: 6
Views: 2,045
Posted By yl01
Gene panel exome data

Hello,

I have got exome sequencing data from 24 samples. It was done on a MiSeq sequencer. The data are not whole exome data, instead it is gene panel of about 200 genes. I have processed the...
Forum: Bioinformatics 03-29-2013, 09:31 AM
Replies: 8
Views: 11,376
Posted By yl01
You don't need a design by yourslef to get the...

You don't need a design by yourslef to get the files of SureSelect v4. You just need to login to the SureDesign web site. The account is free. If you can download the files from somewhere else, I...
Forum: Bioinformatics 03-22-2013, 09:17 AM
Replies: 24
Views: 13,663
Posted By yl01
The outputFile doesn't need to be binary .tdf....

The outputFile doesn't need to be binary .tdf. You can give a file name like myfile.wig, Wig file is a text file.
Forum: Bioinformatics 03-16-2013, 02:31 PM
Replies: 8
Views: 11,376
Posted By yl01
The .bed files are available in SureDesign...

The .bed files are available in SureDesign website. You can find the link of it on eArray entry page. Your eArray login can be used to login to SureDesign. When you have the .bed files, you will see...
Forum: SOLiD 01-21-2013, 08:10 AM
Replies: 2
Views: 2,267
Posted By yl01
BAMstats is a module of LifeScope. You can try to...

BAMstats is a module of LifeScope. You can try to find documentation of it in LifeScope manual. Another QC tool suggested by Life Biotechnologies people is fastQC. It runs on LifeScope produced BAM...
Forum: Bioinformatics 01-06-2013, 08:52 AM
Replies: 2
Views: 894
Posted By yl01
SUMMARIZE_ANNOVAR can do it. See it on the...

SUMMARIZE_ANNOVAR can do it. See it on the annovar homepage.
Forum: Bioinformatics 12-28-2012, 07:44 AM
Replies: 10
Views: 4,584
Posted By yl01
Source Code for biology and medicine could be an...

Source Code for biology and medicine could be an option.
Forum: Bioinformatics 11-07-2012, 02:53 AM
Replies: 8
Views: 11,376
Posted By yl01
Got the answer from Agilent informatics support....

Got the answer from Agilent informatics support. The bed files are available from SureDesign web site, which can be seen from the eArray entry page. The downloaded bed files have 3 tracks: "Target...
Forum: Bioinformatics 11-05-2012, 03:32 AM
Replies: 2
Views: 8,433
Posted By yl01
Thanks Gig77 for the answer! I tested with -e and...

Thanks Gig77 for the answer! I tested with -e and it gave what I wanted.
Forum: Bioinformatics 11-03-2012, 04:18 PM
Replies: 8
Views: 11,376
Posted By yl01
Agilent SureSelect exome enrichment bed file

I was wondering where can I donwload the bed file for the Agilent SureSelect exome enrichment for human. Someone has mentioned eArray web site. Doesn anyone know what keywords should I use to find...
Forum: Bioinformatics 11-03-2012, 03:33 PM
Replies: 2
Views: 8,433
Posted By yl01
Splitting multiple sample vcf file

A question appears when working with vcf file produced by UnifiedGenotyper on multiple samples. It is of course better to work with single sample vcf file so I was trying to split the multiple sampel...
Forum: Bioinformatics 11-03-2012, 03:07 PM
Replies: 6
Views: 2,648
Posted By yl01
Yes, SUMMARIZE_ANNOVAR can just do it. See it on...

Yes, SUMMARIZE_ANNOVAR can just do it. See it on the annovar home page.
Forum: Bioinformatics 09-18-2012, 04:04 AM
Replies: 2
Views: 2,483
Posted By yl01
Thank you vivek_ for poiting out the link. It...

Thank you vivek_ for poiting out the link. It answered my question well. The short answer seems to be multiple sample calling is always better.
Forum: Bioinformatics 09-17-2012, 01:25 PM
Replies: 2
Views: 2,483
Posted By yl01
GATK UnifiedGenotyper question

Hello all,

I was setting up my human exome sequencing analysis pipeline mostly according to the How-to/exome analysis manual. My question is in the producing raw SNP call step using...
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