User: Sophia

gravatar for Sophia
Sophia300
Reputation:
300
Status:
New User
Location:
Barcelona
Last seen:
7 years, 5 months ago
Joined:
9 years, 7 months ago
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Posts by Sophia

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Vcf-Compare Vcftools Error
... do you have the tabix program in your PATH? ...
written 8.4 years ago by Sophia300
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Comment: C: Best Way To Compare Output Snp/Indels From Different Software?
... the publication is available here now: http://bioinformatics.oxfordjournals.org/content/28/3/421.abstract?sid=f64403e7-5050-4102-963c-e690efe003f7 ...
written 8.4 years ago by Sophia300 • updated 9 months ago by RamRS27k
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Comment: C: How To Study Effects Of Mutations
... @liyf: That would depend on the aim of your study. A given variant may have a different impact on different transcripts of the same gene. Each line of the Condel output gives you one variant in one transcript with one prediction of deleteriousness. You could e.g. select transcripts that are likely t ...
written 8.4 years ago by Sophia300
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Comment: C: Gatk Unifiedgenotyper Error:Error: The Number Of Base Qualities Does Not Match T
... does any line of your bam file contain qualities at all? ...
written 8.4 years ago by Sophia300
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Answer: A: Vcftools,--Diff Option
... the perl modules of vcftools include some functionalities that might be of use to you: vcf-compare vcf-isec and more... ...
written 8.5 years ago by Sophia300
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Comment: C: Vcftools,--Diff Option
... Joanne, I just checked out the commands in the documentation at vcftools.sourceforge.net/docs.html and did not find the option you are talking about. Are we talking about the same vcftools program? ...
written 8.5 years ago by Sophia300
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Comment: C: Vcftools,--Diff Option
... Joanne, I just checked out the commands at vcftools documentation and did not find the option you are talking about. Are we talking about the same vcftools program? ...
written 8.5 years ago by Sophia300
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Answer: A: Missense Mutations Predictions Using Sift And Polyphen-2
... There is also Condel , a method that calculates a combined deleteriousness score from the above mentioned methods. It can be run in a web browser from here . ...
written 8.9 years ago by Sophia300
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Answer: A: How Many Human Drug Targets Are There?
... I found that KEGG Drug is a nicely organized resource. For each drug, you can find entries on target genes (TARGET), genes involved with the metabolism (METABOLISM) of the drug and genes interacting with the drug (INTERACTION) in another way. See an example entry here . ...
written 8.9 years ago by Sophia300
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Answer: A: How To Study Effects Of Mutations
... Try also Condel , which combines several of the above mentioned methods variant effect prediction methods. ...
written 8.9 years ago by Sophia300

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