User: Hamid

gravatar for Hamid
Hamid10
Reputation:
10
Status:
New User
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Last seen:
6 months ago
Joined:
3 years, 4 months ago
Email:
h**********@gatech.edu

Posts by Hamid

<prev • 10 results • page 1 of 1 • next >
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(Closed) how can I get the positions of snps for hg19?
... Hey Guys, How can I get the position of the snps given the rs# ? The dbSNP batch is retired, and there is a library cruzdb, which does not work for me. Any other solution to that? ...
gwas snp written 6 months ago by Hamid10
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What are alleles Y, Z
... Hello guys, can someone tell me what does alleles Y and Z mean? For example this is from a tabular file that shows alleles on chromosome 16: 16 rs2443047 0 56208410 T C 16 rs2443046 0 56208600 G A 16 rs77755488 0 56208672 T C 16 rs1120535 0 56209081 ...
gwas aleles written 6 months ago by Hamid10 • updated 6 months ago by Benn7.4k
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PLINK --r2 square: snp ids are not written
... Hey Guys, I'm running plink as bellow plink --r2 square --bfile [file] --out out and what I get is a matrix without any header, then where is the snp ids? How do I know which column correspond to which snp? Thanks ...
snp plink ld r2 written 6 months ago by Hamid10 • updated 6 months ago by chrchang5235.5k
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Answer: A: Annotation format for SNVs
... Thanks, I found the header actually, for now, my main question is why do we have 3 lines per each snp? And what is the Ref and what is the Anc. The header for the first few columns is: Chrom Pos Ref Anc Alt Type Length ...
written 9 months ago by Hamid10
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Annotation format for SNVs
... Hello Biostars, I have a SNV annotations for a number of genes. They look like this: https://ufile.io/hyvs4 Can someone shed some light on this and tell me, 1. Why there are 3 rows for each position? 2. What software generates this type of annotation? 3. What is each column? I assume it is a standa ...
snv snp written 9 months ago by Hamid10
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Comment: A: Any implementation of the edgeR in python
... Thanks man :) Ok, so where is that documentation? ...
written 24 months ago by Hamid10
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Any implementation of the edgeR in python
... Hi Biostars, I wonder if there is an implementation of edgeR calcNormFactors (i.e. normalization) in python. I'm not comfortable with R. Thanks ...
normalization next-gen rna-seq sequencing written 24 months ago by Hamid10 • updated 6 months ago by joonyoon.jay10
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Comment: C: Some basic question on quantification of RNA-seq mapped reads
... Thank you so much for your response. So on 4, does it mean that XS is only reported if a read spans two exons (i.e. a junction)? and if yes, how is it used to determine the likely orientation of a gene? ...
written 2.0 years ago by Hamid10
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Some basic question on quantification of RNA-seq mapped reads
... Hello everyone, I'm trying to use stringtie to quantify some previously mapped RNA-seq reads. And I have some basic questions. I appreciate if someone explains to me in simple words: 1. How does certain quantifier's can only quantify the output of spliced aligners? Does it make any difference? Afte ...
alignment stringtie quantification rna-seq hisat written 2.0 years ago by Hamid10
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Tcga Illumina Methylation Combining 27K And 450K
... Hi everyone, There was a question on this long ago but no detailed answer was given to it, so I rephrase it again. I'm going to use Level 3 methylation data from TCGA database. Part of the cases have normalized methylation counts per million reads derived from 450K and the others from 27. Is it safe ...
dna-methylation rna-seq written 3.4 years ago by Hamid10

Latest awards to Hamid

Popular Question 9 months ago, created a question with more than 1,000 views. For Tcga Illumina Methylation Combining 27K And 450K
Popular Question 24 months ago, created a question with more than 1,000 views. For Tcga Illumina Methylation Combining 27K And 450K

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