User: Dayna

gravatar for Dayna
Dayna10
Reputation:
10
Status:
New User
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Last seen:
10 hours ago
Joined:
6 months, 1 week ago
Email:
d*************@gmail.com

Posts by Dayna

<prev • 31 results • page 1 of 4 • next >
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Comment: C: put a vcf in a library
... so library means just a folder? then i share the folder over ftp, and nothing to do with a vcf? ...
written 13 hours ago by Dayna10
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Comment: C: put a vcf in a library
... me neither. I am asked to put my vcf in a library to be shared via ftp server? ...
written 14 hours ago by Dayna10
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Comment: C: What are the range or ceiling of metrics like DP4 , MQP, etc to filter variant
... that's really helpful Kevin, thank you a lot ...
written 8 weeks ago by Dayna10
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Comment: C: What are the range or ceiling of metrics like DP4 , MQP, etc to filter variant
... Thanks Kevin a lot . But this seems fuzzy logic to me as a beginner, when I look at a number, and I can't even judge to discard or keep as no rule ...
written 8 weeks ago by Dayna10
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Comment: C: What are the range or ceiling of metrics like DP4 , MQP, etc to filter variant
... Some values doesn't exist because this is not gatk pipeline, this samtools and bcftools, like dp4 ..etc. Yes, I understand gatk is better but as a start and for benchmarking, i need to start with samtools. ...
written 8 weeks ago by Dayna10
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What are the range or ceiling of metrics like DP4 , MQP, etc to filter variants?
... Hi Do you know what are the range of the following metrics? When it says bigger is better, I don't know the ceiling to decide, like if the maximum possible value is 1 then 0.9 is big, and if the maximum is 10 or 50 then 0.9 is low. **I am sorry, I am a very beginner.** ##INFO= ##INF ...
variant calling written 8 weeks ago by Dayna10 • updated 8 weeks ago by Kevin Blighe19k
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Do we discard variants with repetitive regions and do these masks mean repetition?
... Hi Do we discard variants that has repetitive parts? For example in this image, are these black masks of tandem repeats means I should discard the variant here? https://ibb.co/cmqBuc thanx [1]: https://ibb.co/cmqBuc ...
vcf genome browser written 9 weeks ago by Dayna10
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How to find if a gene is duplicated?
... Hi Is there a way to know if a gene is duplicated from a vcf file? Or any other way to find if a gene is duplicated? Thanks ...
vcf duplicated genes written 11 weeks ago by Dayna10
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Comment: C: The exon of a variant
... Thanks swbarnes2 and JC :) ...
written 4 months ago by Dayna10
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The exon of a variant
... Hi every one I have a very interesting variant, it aa.change is reported as : SLC2A5:NM_001135585:exon3:c.C142T:p.Q48X,SLC2A5:NM_003039:exon3:c.C142T:p.Q48X,SLC2A5:NM_001328619:exon4:c.C142T:p.Q48X So the cDNA change is c.C142T , p.Q48X. What does it mean to have 3 transcripts and 2 exons? ...
vcf exon written 4 months ago by Dayna10 • updated 4 months ago by JC6.5k

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