User: Hamid
Hamid • 10
- Reputation:
- 10
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- New User
- Location:
- Last seen:
- 1 year, 9 months ago
- Joined:
- 4 years, 7 months ago
- Email:
- h**********@gatech.edu
Posts by Hamid
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... 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? ...
written 21 months ago by
Hamid • 10
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... 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 ...
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... 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 ...
written 22 months ago by
Hamid • 10
• updated
22 months ago by
chrchang523 ♦ 7.4k
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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 2.1 years ago by
Hamid • 10
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... 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 ...
written 2.1 years ago by
Hamid • 10
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... Thanks man :)
Ok, so where is that documentation? ...
written 3.3 years ago by
Hamid • 10
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... Hi Biostars,
I wonder if there is an implementation of edgeR calcNormFactors (i.e. normalization) in python. I'm not comfortable with R.
Thanks ...
written 3.3 years ago by
Hamid • 10
• updated
22 months ago by
joonyoon.jay • 10
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...
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 3.3 years ago by
Hamid • 10
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... 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 ...
written 3.3 years ago by
Hamid • 10
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... 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 ...
written 4.7 years ago by
Hamid • 10
Latest awards to Hamid
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Tcga Illumina Methylation Combining 27K And 450K
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Tcga Illumina Methylation Combining 27K And 450K
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