Forum: Bioinformatics
10-30-2014, 09:45 AM
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Replies: 4
Views: 2,057
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Forum: Bioinformatics
10-28-2014, 03:52 AM
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Replies: 4
Views: 2,057
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...
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Forum: General
01-27-2014, 01:07 PM
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Replies: 11
Views: 16,068
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.
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Forum: General
01-27-2014, 12:56 PM
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Replies: 3
Views: 5,974
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Forum: Bioinformatics
11-28-2013, 04:17 AM
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Replies: 9
Views: 6,742
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.
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Forum: Bioinformatics
10-25-2013, 07:15 PM
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Replies: 3
Views: 2,623
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Forum: Bioinformatics
09-27-2013, 05:53 AM
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Replies: 0
Views: 1,226
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....
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Forum: Bioinformatics
09-26-2013, 04:52 AM
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Replies: 1
Views: 3,650
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Forum: Bioinformatics
09-20-2013, 02:08 AM
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Replies: 1
Views: 3,650
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...
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Forum: Bioinformatics
04-18-2013, 06:48 AM
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Replies: 6
Views: 2,046
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Forum: Bioinformatics
04-16-2013, 01:33 PM
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Replies: 6
Views: 2,046
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Forum: Bioinformatics
04-16-2013, 07:25 AM
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Replies: 6
Views: 2,046
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...
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Forum: Bioinformatics
03-29-2013, 09:31 AM
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Replies: 8
Views: 11,377
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...
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Forum: Bioinformatics
03-22-2013, 09:17 AM
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Replies: 24
Views: 13,665
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Forum: Bioinformatics
03-16-2013, 02:31 PM
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Replies: 8
Views: 11,377
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...
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Forum: SOLiD
01-21-2013, 08:10 AM
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Replies: 2
Views: 2,269
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Forum: Bioinformatics
01-06-2013, 08:52 AM
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Replies: 2
Views: 894
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Forum: Bioinformatics
12-28-2012, 07:44 AM
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Replies: 10
Views: 4,584
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Forum: Bioinformatics
11-07-2012, 02:53 AM
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Replies: 8
Views: 11,377
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Forum: Bioinformatics
11-05-2012, 03:32 AM
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Replies: 2
Views: 8,434
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Forum: Bioinformatics
11-03-2012, 04:18 PM
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Replies: 8
Views: 11,377
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...
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Forum: Bioinformatics
11-03-2012, 03:33 PM
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Replies: 2
Views: 8,434
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...
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Forum: Bioinformatics
11-03-2012, 03:07 PM
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Replies: 6
Views: 2,648
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Forum: Bioinformatics
09-18-2012, 04:04 AM
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Replies: 2
Views: 2,483
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Forum: Bioinformatics
09-17-2012, 01:25 PM
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Replies: 2
Views: 2,483
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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