User: Sharon
Sharon • 340
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Posts by Sharon
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2
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... Hi everyone
Do you know if the genes starting with Gm in **mouse** have a canonical name or not? I am stuck with those when I used gencode transcripts and gencode gtf for annotations too.
My understanding is they don't have a canonical name yet.
But some of them is mentioned to have overlap with ...
written 4 months ago by
Sharon • 340
• updated
4 months ago by
Emily_Ensembl ♦ 16k
0
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1
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... Thanks WouterDeCoster :) ...
written 4 months ago by
Sharon • 340
4
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1
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157
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1
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... Hi Everyone
If we test the cummulative effect of a group of variants in a gene (or a region) using burden test and association analysis stuff.
If a gene is found very significant, should we validate all variants in the gene using sanger sequence? Doesn't seem reasonable, so what we can do to prove ...
written 4 months ago by
Sharon • 340
• updated
4 months ago by
WouterDeCoster ♦ 33k
1
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1
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410
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... work doesn't leave me =D I just switched to something else :) :) ...
written 4 months ago by
Sharon • 340
0
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1
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410
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... Hi Kevin
Thanks so much and sorry for the late reply, was away.
Yes, this makes sense. I understand where the problem came from but did not how to solve, am still learning R.
I will try that. Thanks so much :) ...
written 4 months ago by
Sharon • 340
5
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1
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410
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... Hi All
How to use tximport with gencode?
I used Gencode transcripts for mouse looks like this:
>ENSMUST00000193812.1|ENSMUSG00000102693.1|OTTMUSG00000049935.1|OTTMUST00000127109.1|RP23-271O17.1-001|RP23-271O17.1|1070|TEC|
AAGGAAAGAGGATAACACTTGAAATGTAAATAAAGAAAATACCTAATAAAAATAAATAA ...
written 4 months ago by
Sharon • 340
• updated
4 months ago by
Kevin Blighe ♦ 31k
0
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1
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251
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... Just in case some one is new to SNP array like me, I found this tutorial, and it is interesting and very helpful:
https://onlinelibrary.wiley.com/doi/full/10.1002/sim.6605 ...
written 5 months ago by
Sharon • 340
0
votes
1
answer
251
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1
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... Hi everyone
I would like to double check my naive steps to analyze SNP-Array data to detect variants associated with a specific phenotypes with you. It is my first go with this data.
1. I converted illumina report to plink format using genome studio.
2. Then I converted plink format to vcf.
3. ...
written 5 months ago by
Sharon • 340
0
votes
0
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136
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... Hi Everyone
Is there a way to detect phenocopies -computationally-, like could linkage analysis help or any other method I am oblivious of?
We have an interesting variant x segregating in all affected from gene G. But for one patient we have variant y from the same gene but not x. I was thinking i ...
written 5 months ago by
Sharon • 340
0
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0
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269
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... Thanks genomax. I also took a look to those posts but still not clear though :( ...
written 5 months ago by
Sharon • 340
Latest awards to Sharon
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Heatmap for differential gene expressions
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Kinship Relatedness using plink
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Kinship Relatedness using plink
Scholar
5 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Coverage in whole genome sequencing
Voter
8 months ago,
voted more than 100 times.
Scholar
11 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Centurion
11 months ago,
created 100 posts.
Scholar
11 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Scholar
11 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Scholar
11 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Scholar
11 months ago,
created an answer that has been accepted.
For A: Alignment dropped with Salmon
Supporter
12 months ago,
voted at least 25 times.
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