User: Nandini

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Nandini720
Reputation:
720
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Location:
London
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Last seen:
1 day, 17 hours ago
Joined:
6 years, 7 months ago
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n********************@gmail.com

Bioinformatician

Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis

Posts by Nandini

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Comment: C: GWAS data analysis strategy or pipeline
... Most of it depends on the aim of your project. What are you trying to achieve from your GWAS study ? Is there an aim to this project ? ...
written 29 days ago by Nandini720
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Comment: C: Alzheimer's disease and its classification
... all SNPs in IGAP identified to date are "susceptible loci" -> meaning there are mostly likely to be associated with a RISK of developing late onset Alzheimer's . The link in my comment above gives you the data or the summary statistics for IGAP. IGAP was a big study that constituted of many many ...
written 29 days ago by Nandini720
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Comment: C: Alzheimer's disease and its classification
... Have you tried GEO or dbGAP ? Also, why are you using a subset of IGAP only ? All of IGAP summary stats are here : [IGAP][1] [1]: http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php ...
written 4 weeks ago by Nandini720
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Comment: C: Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
... thank you @lffu_0032 , the link provided is useful! ...
written 4 weeks ago by Nandini720
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Comment: C: Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
... Yes, done that [already][1] [1]: https://gatkforums.broadinstitute.org/gatk/discussion/13553/difference-in-haplotype-caller-gatk4-vs-3-7#latest ...
written 5 weeks ago by Nandini720
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Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
... Hello Does anyone know the difference/updates for Haplotypecaller in GATK v4 vs GATK 3.7 ? I am not able to find anything specific in terms of its algorithm or major changes in the walker on the GATK website Thanks, ...
haplotypecaller gatk written 5 weeks ago by Nandini720 • updated 4 weeks ago by lffu_003230
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Comment: C: CNV and pseudogenes
... well we are still doing MLPA. Cannot rely on an invalidated CNV pipeline ...
written 11 weeks ago by Nandini720
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Comment: C: CNV and pseudogenes
... of course, we MLPA everything before reporting but also trying to build a reliable bioinformatics pipeline ...
written 11 weeks ago by Nandini720
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Comment: C: CNV and pseudogenes
... True, I agree but we are more in a clinical setting than research so its generating data per panels.. i guess it's just finding an appropriate way of deal with this in a diagnostic environment ...
written 11 weeks ago by Nandini720
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CNV and pseudogenes
... Hello, I'm using ExomeDepth to detect CNVs and I'm providing a bed file for all our targeted gene panels. We know there is a processed pseudogene in a region, am just wondering if this would confound CNV calling in other genes? If it knocks off the ‘average’ coverage ? Is it worth excluding su ...
pseudogenes ngs cnv exomedepth written 11 weeks ago by Nandini720

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 8 weeks ago, created a question with more than 5,000 views. For How to interpret heterozygosity rate ?
Great Question 8 weeks ago, created a question with more than 5,000 views. For Calculate z-scores from GWAS summary stats
Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Epic Question 5 months ago, created a question with more than 10,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 7 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 7 months ago, created a question with more than 1,000 views. For extract SNPs from compressed PLINK files
Popular Question 8 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 9 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Appreciated 9 months ago, created a post with more than 5 votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
Scholar 9 months ago, created an answer that has been accepted. For A: where to get the gene annotations for the latest build 37 - for plotting regiona
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format
Popular Question 10 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Scholar 11 months ago, created an answer that has been accepted. For A: where to get the gene annotations for the latest build 37 - for plotting regiona
Popular Question 12 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
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Popular Question 12 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 22 months ago, created a question with more than 1,000 views. For Convert .Pre Files To .Ped And .Map Files For Plink
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Great Question 2.4 years ago, created a question with more than 5,000 views. For Whole Genome Analysis Pipeline (Illumina)
Great Question 2.4 years ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq

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