User: prasundutta87

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prasundutta87390
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Posts by prasundutta87

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Comment: C: Annotating variants using latest version fof the genome
... Thanks all..I believe that I have got an answer to my query and I am thinking in the right direction! ...
written 1 day ago by prasundutta87390
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Comment: C: Annotating variants using latest version fof the genome
... As an hypothetical example, yes, that's exactly what I am asking and I am hoping that the coordinates will all screw up giving all sort of wrong annotations.. ...
written 1 day ago by prasundutta87390
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Annotating variants using latest version fof the genome
... Hi, I have SNP data from an array which has coordinate information from an older version of the genome (in VCF form). I want to annotate it using GTF/GFF file of the current version of the genome using SnpEff or ANNOVAR or VEP. Do I need to take care of the VCF coordinates somehow (like liftover) s ...
vcf snp written 1 day ago by prasundutta87390
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Comment: C: Identifying Private SNPs between multi sample vcf files.
... Check this out: https://pcingola.github.io/SnpEff/SnpSift.html#private Hope this helps. ...
written 10 weeks ago by prasundutta87390
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rare SNP or SNV
... Hi, Can a rare variant (point mutation) be called a rare SNP (single nucleotide polymorphism) or instead should be called a rare SNV (single nucleotide variant)? This is because the word 'SNP' refers to single base variations that have risen to a frequency greater than 1% of the population. Just to ...
snv snp written 10 weeks ago by prasundutta87390
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find tabix version
... Hi, Is there any way to find the version of tabix used to make a .tbi file for an associated vcf.gz file? Regards, Prasun ...
software vcf tabix written 11 weeks ago by prasundutta87390
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Comment: C: methylation % calculation for targeted region
... Hi, Thanks for your reply. I just wanted to get methylation % as of now..but I have got a reply now..you can go to this link to find the answer, was meaning to post it anyway here: https://github.com/FelixKrueger/Bismark/issues/354 ...
written 4 months ago by prasundutta87390
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Comment: C: methylation % calculation for targeted region
... Cross-posting in main GitHub for bismark page, hopefully, will get a reply there. ...
written 4 months ago by prasundutta87390
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methylation % calculation for targeted region
... Hi, I want to get the **average methylation % for a targeted region**, for example, see below... Chrom start end Meth_% count_methylated count _unmethylated chr1 1371409 1371409 0 0 5 chr1 1371539 1371539 0 0 88 chr1 1371567 1371567 2.32 2 ...
methylation written 4 months ago by prasundutta87390
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Comment: C: EPIC methylation manifest GRch38 query
... Found the answer myself, it turns out that its 0-based, however, when pasted in UCSC genome browser, 3 nucleotides come up, but that's because the browser runs on the 1-based coordinate system. ...
written 4 months ago by prasundutta87390

Latest awards to prasundutta87

Popular Question 11 days ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Popular Question 8 weeks ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Great Question 3 months ago, created a question with more than 5,000 views. For fastqc adapter content
Popular Question 3 months ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Popular Question 4 months ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Popular Question 4 months ago, created a question with more than 1,000 views. For variant annotation issue
Popular Question 7 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 8 months ago, created a question with more than 1,000 views. For Correct way to report variant statistics from bcftools stats report
Popular Question 9 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 11 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 11 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 12 months ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 13 months ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 13 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Student 14 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
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Popular Question 20 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
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Scholar 23 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 2.0 years ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 2.1 years ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 2.1 years ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 2.2 years ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 2.3 years ago, created 100 posts.

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