User: jan
jan • 90
- Reputation:
- 90
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- Trusted
- Location:
- Malaysia
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 3 years, 10 months ago
- Email:
- j**********@gmail.com
Posts by jan
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... Hi,
I want to include number of papers cited a certain journal (can be obtained from google scholar) and the journal current impact factor to my references.
Is there a tool to export such information from google scholar to endnote? or Excel, or any relevant working sheet. I have 300+ citations t ...
written 12 weeks ago by
jan • 90
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... I ended up following above suggestion. MAF (mutation allele format) is a format of my variant file. My sequencing vcf files were initially anonated with snpEff and in-house qSNP.
So what we did was to re-annotate vcf files using VEP and use their ExAC plugin which can calculate frequency from AN, ...
written 7 months ago by
jan • 90
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A: annotating strand orientation
... HI,
My VCF has information regarding the strandbias which is not what Im asking.
What I need to know is the orientation of the transcripts , either on forward or reverse direction. eg BRCA1 transcript is on the reverse transcript. I have looked in my VCF and it's missing the transcript orientation ...
written 14 months ago by
jan • 90
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... Is there a way to annotate my VCF with the transcript orientation ?
Is there any reference for strand orientation ?
...
written 14 months ago by
jan • 90
• updated
14 months ago by
prasundutta87 • 300
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Comment:
C: tips for checking variants in IGV
... Thank you for your feedback. Apart from that, I would also like to know what kind of parameters should I set ?
For example in View > Alignments ; there are few options such as Alignment Track Options (particularly mapping quality threshold), Coverage Track options, etc?
Is it ok if I just leav ...
written 20 months ago by
jan • 90
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... Hi,
I need to check some germline variants on IGV from BAM files based on their positions.
Is there a good tutorial/guide on how to set up parameters/filters in IGV and the reasoning behind them?
Im only aware of the basic parameters such as strand-bias, variant on >20% reads.
...
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... HI,
I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all population in Exac.
I have used awk script to match my variants in MAF files with the VCFs from EXac database. However, Exac only provides the allele count and allele number (AC ; AN) for population specific ...
written 2.0 years ago by
jan • 90
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... Hi,
Im trying to find the MSI-status for TCGA samples and couldn't find the information in clinical/clinical supplement and biospecimen/biospecimen supplement files.
What i need looks something like this:
https://wiki.nci.nih.gov/display/TCGA/Microsatellite+data
Where can I find these informati ...
written 2.2 years ago by
jan • 90
• updated
2.2 years ago by
Shicheng Guo • 7.3k
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... Thank you for the information,
However, most of the tools are designed to predict nonsynonymous missese based on multiple sequence alignment i.e variants at conserved site are likely to have larger functional impact. And also some other algorithms that make use protein biochemical properties, domai ...
written 2.3 years ago by
jan • 90
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992
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... Hi,
Is there any good prediction tools that can predict deliriousness of nonsense variants?
Im trying to prioritize germline variants that might be potentially pathogenic to the disease that I'm investigating. After filtering for rare variants, and my genes of interest, i still have quite a numbe ...
written 2.3 years ago by
jan • 90
• updated
2.3 years ago by
Chris Cole • 680
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