User: nkausthu

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nkausthu20
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Posts by nkausthu

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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 4 weeks ago by nkausthu20
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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 4 weeks ago by nkausthu20 • updated 19 days ago by Kevin Blighe49k
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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 4 months ago by nkausthu20
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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 4 months ago by nkausthu20
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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 9 months ago by nkausthu20 • updated 9 months ago by Kevin Blighe49k
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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 13 months ago by nkausthu20
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How to order biostar handbook professional version
... Hi, I would like to order Biostar handbook professional version. where it will be available ? ...
biostar handbook written 13 months ago by nkausthu20 • updated 13 months ago by jared.andrews073.4k
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Identification of break points for a balanced translocation
... Hi, From the karyotype results we could see a balanced translocation in one of the sample and we have whole genome data available for the same sample. It would be really great if someone can give suggestion in this regard. We have extracted the clipped reads aligned to both the chromosome and part ...
balanced translocation wgs breakpoint analysis written 13 months ago by nkausthu20 • updated 13 months ago by Pierre Lindenbaum123k
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Comment: C: Extraction of partially mapped reads from BAM
... I used samextractclip.jar and converted clipped part of the reads into fastq file. Actually I am trying to figure out the breakpoints for a balanced translocation using these reads. Could you please give some suggestion in this regard. ...
written 13 months ago by nkausthu20
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Comment: C: Extraction of partially mapped reads from BAM
... Thank you so much and I could retrieve partially mapped reads using samjdk. I have one more query, I want to retrieve the part of the read sequences which are soft-clipped. Any tools are available for this or do I need to write the code for the same. ...
written 13 months ago by nkausthu20

Latest awards to nkausthu

Popular Question 4 months ago, created a question with more than 1,000 views. For Tools for visualization of CNVs called by XHMM
Popular Question 9 months ago, created a question with more than 1,000 views. For Annotation of XHMM VCF file (CNV analysis)
Popular Question 9 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 11 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 11 months ago, created a question with more than 1,000 views. For Number of homozygous and heterozygous variants

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