User: nkausthu

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nkausthu20
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4 months, 1 week ago
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2 years, 8 months ago
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Posts by nkausthu

<prev • 43 results • page 1 of 5 • next >
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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 4 months ago by nkausthu20 • updated 4 months ago by Kevin Blighe42k
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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 8 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 8 months ago by nkausthu20 • updated 8 months ago by jared.andrews072.3k
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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 8 months ago by nkausthu20 • updated 8 months ago by Pierre Lindenbaum120k
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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 8 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 8 months ago by nkausthu20
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Extraction of partially mapped reads from BAM
... Hi, It would be great if anyone can give some suggestion on extracting partially mapped reads from bam/sam generated using BWA or articles which describes more about partially mapped reads. Thank you. ...
partially mapped reads bam bwa written 8 months ago by nkausthu20 • updated 8 months ago by Pierre Lindenbaum120k
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Comment: C: extractPIRs is throwing an ERROR
... Yes .. Programs tells that its duplicate site position but its in different chromosome. But I think it wont be correct if I delete one. ...
written 13 months ago by nkausthu20
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extractPIRs is throwing an ERROR
... I am getting an error while using extractPIRs as follows ./extractPIRs --bam bamlist --vcf VCF.gz --out Reading genotypes in [/MOD_recalibrated_variants.vcf.gz] in VCF format * 477 samples ERROR: Duplicate site pos=52264013 ref=C alt=T How can I avoid this kind of scenario? ...
shapeit extractpirs phasing written 13 months ago by nkausthu20 • updated 13 months ago by genomax67k
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Identification of Common ROH region between two exomes
... Can anyone suggest me the best method to identify common ROH region between two exomes. I have the vcf files for both the samples and I initially used FILTUS but when I cross check FILTUS results manually, I could find heterozygous variants with in the ROH region given by FILTUS. Then I used bcftoo ...
exome roh bcftools filtus written 13 months ago by nkausthu20 • updated 13 months ago by Biostar ♦♦ 20

Latest awards to nkausthu

Popular Question 6 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 6 months ago, created a question with more than 1,000 views. For Number of homozygous and heterozygous variants

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