User: Amirosein

gravatar for Amirosein
Amirosein70
Reputation:
70
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Trusted
Location:
UBC, Vancouver, CA.
Last seen:
1 year, 3 months ago
Joined:
3 years, 11 months ago
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Posts by Amirosein

<prev • 40 results • page 3 of 4 • next >
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How to make new VCF files myself?
... Hi I'm doing some computations on sanger seq. data. for example i have a read, i aligned it to the reference genome and found an SNP, now i want to make a new VCF file for using in other tools like Annovar or SIFT, how to do this? (specially in Rstudio/Bioconductor) "VcfR" is not published yet an ...
vcf variant variantannotation written 3.5 years ago by Amirosein70 • updated 3.4 years ago by chen1.9k
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Comment: C: Finding the Length Distribution of Structural Variations
... common! kidding me? polypeakparser is a software to find heterozygous indels in sanger reads but not for structural variation detection. ...
written 3.5 years ago by Amirosein70
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Comment: C: How To Call Snp From .Ab1 Files Of Sanger Sequencing?
... only for SNP calling? is it able to find all point mutations or/and indels? ...
written 3.5 years ago by Amirosein70
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Variant calling for sanger reads
... Hello all i have a Sanger read (an *.ab1 file which i did basecalling for it) and a reference. i want to find homo and hetero events for this sample (read) for further computations like annotating individual variants. now i did it myself but it seems there is a standard pipeline for this purpose for ...
sanger alignment variantcalling variants written 3.5 years ago by Amirosein70 • updated 3.5 years ago by Keith Callenberg900
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Answer: A: Finding the Length Distribution of Structural Variations
... Poly Peak Parser will do it published 2014 with this title: Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. it can find positions that deletions occurred in one of two sequenced strings ...
written 3.8 years ago by Amirosein70
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Comment: C: detection of in/del in sanger sequencing
... ok thanks, i'll check again :) ...
written 3.8 years ago by Amirosein70
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Comment: C: detection of in/del in sanger sequencing
... as i know, Polyphred could not handle Indels but only handle Substitutions. ...
written 3.8 years ago by Amirosein70
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Comment: C: Finding the Length Distribution of Structural Variations
... i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, ""where to find the length of Structural Variation?"" thanks ...
written 3.8 years ago by Amirosein70
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Comment: C: Finding the Length Distribution of Structural Variations
... yeah i need the regions, so where to get them? ...
written 3.8 years ago by Amirosein70
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Comment: C: Finding the Length Distribution of Structural Variations
... i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, where to find the length of Structural Variation? thanks ...
written 3.8 years ago by Amirosein70

Latest awards to Amirosein

Popular Question 15 months ago, created a question with more than 1,000 views. For detection of in/del in sanger sequencing
Popular Question 24 months ago, created a question with more than 1,000 views. For importing .SAM files into R (Rstudio)
Popular Question 24 months ago, created a question with more than 1,000 views. For how to add lines to a plot gradually (ggplot2) ?
Popular Question 24 months ago, created a question with more than 1,000 views. For Variant calling for sanger reads
Scholar 3.8 years ago, created an answer that has been accepted. For A: Retrieving overlaps inside a single dataset using foverlaps

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