User: Nandini

gravatar for Nandini
Nandini660
Reputation:
660
Status:
Trusted
Location:
London
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
6 years, 4 months ago
Email:
n********************@gmail.com

Bioinformatician

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

Posts by Nandini

<prev • 177 results • page 1 of 18 • next >
0
votes
0
answers
47
views
0
answers
Comment: C: CNV and pseudogenes
... of course, we MLPA everything before reporting but also trying to build a reliable bioinformatics pipeline ...
written 2 hours ago by Nandini660
0
votes
0
answers
47
views
0
answers
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 2 hours ago by Nandini660
0
votes
0
answers
47
views
0
answers
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 6 hours ago by Nandini660
0
votes
0
answers
73
views
0
answers
Comment: C: Tools to detect CNV for NGS-mtDNA
... okay, i'll try out a couple of CNV callers. ...
written 8 days ago by Nandini660
0
votes
0
answers
73
views
0
answers
Comment: C: Tools to detect CNV for NGS-mtDNA
... yes, its only the mtDNA that has been sequenced entirely . Does Lumpy include the breakpoints info for each CNV detected ? ...
written 8 days ago by Nandini660
0
votes
0
answers
73
views
0
answers
Tools to detect CNV for NGS-mtDNA
... Hello, Wondering if there are tools to detect CNV (duplications and deletions) for mitochondrial NGS analysis (clinical setting) ? Not sure if I can use ExomeDepth for the same ? Thank you ...
mtdna tools ngs written 8 days ago by Nandini660
0
votes
2
answers
455
views
2
answers
Comment: C: Detection of deletion for mitochondrial NGS analysis at position 3107
... Hi MatthewP, So I use varscan `mpileup2SNP` and `mpileup2indel` and then combine the two result files, followed by annotation. If you are using GATK, then I THINK you can use GATK's Mutect rather than Haplotypecaller (though I do not have much experience with GATK and mtDNA analysis) ...
written 16 days ago by Nandini660
0
votes
1
answer
189
views
1
answers
Comment: C: Next-Seq sequences map poorly to ref genome
... if it says `95` then its quite low. Its under clustered ...
written 26 days ago by Nandini660
0
votes
1
answer
159
views
1
answers
Comment: C: Down sampling BAM files for CNV detection
... Thanks Both. Another quick question, is there a way to select the seed or is it totally random ? ...
written 26 days ago by Nandini660
0
votes
1
answer
159
views
1
answers
Comment: C: Down sampling BAM files for CNV detection
... so does this means "S" sets the seed of 0 and only 10% of the reads by samtool ? I was going to to use sambamba for downsampling but I guess they are both similar - PE mates are lost, I think on downsampling ...
written 26 days ago by Nandini660

Latest awards to Nandini

Popular Question 2 days ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 5 days ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Epic Question 10 weeks ago, created a question with more than 10,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 4 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 4 months ago, created a question with more than 1,000 views. For extract SNPs from compressed PLINK files
Popular Question 5 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Great Question 6 months ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Appreciated 6 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 6 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 6 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 6 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 8 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Scholar 8 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 9 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Centurion 9 months ago, created 100 posts.
Popular Question 9 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 16 months ago, created a question with more than 1,000 views. For How to interpret heterozygosity rate ?
Popular Question 19 months ago, created a question with more than 1,000 views. For Convert .Pre Files To .Ped And .Map Files For Plink
Popular Question 21 months ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Great Question 2.2 years ago, created a question with more than 5,000 views. For Whole Genome Analysis Pipeline (Illumina)
Great Question 2.2 years ago, created a question with more than 5,000 views. For Pros and cons of Illumina HiSeq and Next Seq
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Low Coverage Depth On Exome Sequencing

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1894 users visited in the last hour