User: prasundutta87

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prasundutta87300
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Posts by prasundutta87

<prev • 146 results • page 1 of 15 • next >
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Comment: C: Difference between Private SNPs and Singleton SNPs
... I used the GATK germline variant calling pipeline to generate my VCF file. Is any more information needed? ...
written 4 days ago by prasundutta87300
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Comment: C: Difference between Private SNPs and Singleton SNPs
... Thanks Giovanni. Do you know how are Private variants found or how they are assigned to a population in a VCF file? I know that Snpsift has a tool called 'private' that does that. But do you know what methodology does it follow to achieve that? ...
written 4 days ago by prasundutta87300
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Difference between Private SNPs and Singleton SNPs
... Hi, I was wondering if anyone can let me know the difference between 'Private' SNPs and 'Singleton' SNPs in a VCF file. For example, if I have a multisample VCF file of 20 samples, containing samples from different populations/families..say family A and family B each consisting of 10 individuals ea ...
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Correct way to report variant statistics from bcftools stats report
... Hi, I am making a table of family-wise variants statistics. I have a multisample VCF file of biallelic SNPs on which I ran BCFtools v1.6 using the following command. bcftools stats -s - This gives me the following output (edited for brevity): sample nRefHom nNonRefHom nHets family_ ...
bcftools snp variants statistics written 6 days ago by prasundutta87300
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Comment: C: PCAtools: everything Principal Components Analysis
... Understandable..Thanks a lot Kevin.. ...
written 10 days ago by prasundutta87300
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Comment: A: PCAtools: everything Principal Components Analysis
... Great package..but why does it want only R 3.6..It's not even officially released. ...
written 10 days ago by prasundutta87300
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Answer: A: Paired-end flag for singleton
... I believe when a read is singleton, it is 'unpaired' for a paired-end sequencing read. So, you can check for reads whose flags are not set to 1 which is the flag for 'paired-end' reads.. ...
written 3 months ago by prasundutta87300
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Comment: C: manhattan plot with Fst values
... Right..you need to import your input data in R first before you do anything with it... ...
written 3 months ago by prasundutta87300
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Comment: A: manhattan plot with Fst values
... Please post your whole code here. How have you imported the data in R? ...
written 3 months ago by prasundutta87300
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Comment: C: no gene_id for tRNA in GFF3
... I could only moderate my post to make it as an 'answer'..the main answer should be your first reply.. ...
written 3 months ago by prasundutta87300

Latest awards to prasundutta87

Scholar 5 weeks ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Popular Question 9 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 11 weeks ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 4 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 4 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 5 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 6 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 7 months ago, created 100 posts.
Supporter 9 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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