User: nkausthu

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nkausthu30
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3 years, 11 months ago
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Posts by nkausthu

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Exome data processing and variant calling based on GRCH38
... Yes, I had gone through this article. I am looking if anyone can give specific answer for the following concerns 1) In a clinical context would the alt-aware alignment will make a huge impact on the downstream analysis 2) what is the impact of considering only primary assembly as a reference. Are w ...
written 7 weeks ago by nkausthu30
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Exome data processing and variant calling based on GRCH38
... Hi I am basically working on rare monogenic disorders and now we are in process of shifting the reference to GRCh38 for exome sequencing data analysis. I am not very sure whether I should go for an alt-aware alignment or I can just focus on primary assembly and call the variants. I had come across ...
variant calling grch38 alt-aware alignment written 7 weeks ago by nkausthu30 • updated 7 weeks ago by WouterDeCoster44k
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Comment: C: Alignment of reads to gene and pseudogene
... So which means when the aligner is not able to find a single optimal alignment, it randomly choose the location to map the read?. In my case the reads with the variant aligned to gene and the reads with out the variant aligned to pseudogene is just by chance, am I correct? . But I am not understandi ...
written 9 weeks ago by nkausthu30
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Alignment of reads to gene and pseudogene
... ![MSA][1] Hi, It would be great, if anyone can help me to understand how bwa-mem alignment works when there is a pseudogene. When there is a region of gene which is 100% similar to the pseudogene and the generated reads are with a variant, then how the aligner will be able to map the reads to the ...
gene pseudogene alignment mapping quality bwa written 9 weeks ago by nkausthu30
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Comment: C: Generation of incorrect heterozygous calls after left normalization using bcftoo
... I can provide vcf file after left normalization is that sufficient? ...
written 12 months ago by nkausthu30
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Generation of incorrect heterozygous calls after left normalization using bcftools
... I have following records in one of the gvcf file 1 3753032 . GTTTT G,GT,GTTT,GTTTTT,GTTTTTT,GTTTTTTTT, 1 10502954 . CTTTTT C,CT,CTTT,CTTTT,CTTTTTT, 1 11272829 . T 1 11272839 . G ...
left normalization multiallelic sites bcftools written 12 months ago by nkausthu30 • updated 11 months ago by Kevin Blighe65k
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Comment: C: Why bcftools + guess-ploidy is not giving the correct results
... I had seen 10k reads aligned to y for a female exome data. I don't know the cutoff for number of reads to consider to be significant or not. ...
written 15 months ago by nkausthu30
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Why bcftools + guess-ploidy is not giving the correct results
... Hi, I have used bcftools +guess-ploidy on some of the vcf files but every sample is predicted as females. How to correct this? Or any other easy method available to guess the gender based on exome data. Thanks in advance. ...
bcftools guess-ploidy written 15 months ago by nkausthu30
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SPANR result interpretation
... Hi, I have an intronic variant which lies ~70bp upstream of an exon and I have used splicing-based Analysis of Variants (SPANR) to know the impact of a an intronic variant. Unfortunately, I am unable to interpret the results given and not able to find any tutorial regarding the tool. It would be re ...
spanr intronic variant impact on splicing written 20 months ago by nkausthu30 • updated 20 months ago by Kevin Blighe65k
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Comment: C: Identification of break points for a balanced translocation
... Thank you and I ran Delly for the paired end data. But its taking too much of time to give the results. As I have the karyotype results can I specify the specific chromosomes and run Delly? ...
written 2.0 years ago by nkausthu30

Latest awards to nkausthu

Popular Question 12 months ago, created a question with more than 1,000 views. For Tools for visualization of CNVs called by XHMM
Popular Question 12 months ago, created a question with more than 1,000 views. For Detection of CNVs
Popular Question 15 months ago, created a question with more than 1,000 views. For Tools for visualization of CNVs called by XHMM
Popular Question 20 months ago, created a question with more than 1,000 views. For Annotation of XHMM VCF file (CNV analysis)
Popular Question 20 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 22 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 22 months ago, created a question with more than 1,000 views. For Number of homozygous and heterozygous variants

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