User: Doctoroots

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Doctoroots790
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Posts by Doctoroots

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Comment: C: Structural Variations (Sv) Annotation Workflow
... hi raymond, although the tool looks useful for other purposes i couldnt see how it handles structural variants such as translocations and inversions ...
written 8.6 years ago by Doctoroots790
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Answer: A: Gatk Unifiedgenotyper Error:Error: The Number Of Base Qualities Does Not Match T
... A good place to post questions and find answers regarding GATK is their support forum : GSA get satisfaction i found some related questions to your problem, this one has a suggested solution: UnifiedGenotyper over BAM files without base qualities and heres another question dealing with this issue E ...
written 8.7 years ago by Doctoroots790
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Structural Variations (Sv) Annotation Workflow
... I want to know if there is some kind of pipeline i can use in order to annotate a given list of structural variants detected by NGS. specifically, i just ran Breakdancer on a paired end sequencing data and recieved the output specifying the different types of predicted variations (insertions / dele ...
annotation workflow structural written 8.7 years ago by Doctoroots790 • updated 8.7 years ago by Raymond301160
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Comment: C: How To Demultiplex Mate Paired Reads When You Have Only One Index?
... i would change the title to be a bit more specific, something like : how to demultiplex paired end reads with one index file? ...
written 8.7 years ago by Doctoroots790
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Answer: A: How To Demultiplex Mate Paired Reads When You Have Only One Index?
... Considering the details given, i dont have alot to offer, but you can try this tool : FastqMultx with the -g option for the reads index file. it should demultiplex both files. ...
written 8.7 years ago by Doctoroots790
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Answer: A: Finding Isomirs In Alingnment Files. Next Steps After Mapping To The Pre-Mirnano
... Ive just preformed a very similar analysis, basically i wanted to look at the isomiR population in my sequenced data so i preformed the following steps: create a reference file of the mature miR sequnces with a flanking region on both 5 and 3 prime ends (i chose flank=3 bases) collapse the seque ...
written 8.8 years ago by Doctoroots790
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Answer: A: Maximum Read Depth
... generally, maximal coverage for variant calling is set out of memory considerations, for this purpose i think the practice recommended in the GATK Unified Genotyper should be appropriate: "...When running on projects with many samples at low coverage (e.g. 1000 Genomes with 4x coverage per sample) w ...
written 8.8 years ago by Doctoroots790
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Comment: C: Small Rna (Mirna) Mapping
... i think you meant -n 0 ...
written 8.8 years ago by Doctoroots790
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Answer: A: Annovar And String Problems
... A possible solution is using the region annotation option in Annovar. basically, treating the dbsnp file as a region file will result in location comparison without considering the alleles. the command will look like this: annotate_variation.pl -regionanno -dbtype snp132 -buildver hg19 mySNPs humand ...
written 8.8 years ago by Doctoroots790
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Answer: A: Indel Annotation Tools, Not Loss Of Function
... You should take a look at other SNP annotation related questions: SNP location annotation variant effect predictor / annotator In my experience, Annovar is very easy to use, well documented, supports various SNP file formats and provides flexibility in regards to the different types of supported ann ...
written 8.8 years ago by Doctoroots790 • updated 13 months ago by RamRS30k

Latest awards to Doctoroots

Supporter 7.5 years ago, voted at least 25 times.
Voter 7.5 years ago, voted more than 100 times.
Student 8.7 years ago, asked a question with at least 3 up-votes. For Structural Variations (Sv) Annotation Workflow
Teacher 8.7 years ago, created an answer with at least 3 up-votes. For A: How To Demultiplex Mate Paired Reads When You Have Only One Index?
Popular Question 9.2 years ago, created a question with more than 1,000 views. For Copy Number Variation (Cnv) Detection Using Single-End Sequencing Data
Teacher 9.5 years ago, created an answer with at least 3 up-votes. For A: Snp Indel Discovery - Critique A Proposed Workflow
Teacher 9.5 years ago, created an answer with at least 3 up-votes. For A: Converting Bam To Fastq
Good Question 9.6 years ago, asked a question that was upvoted at least 5 times. For In Deep Sequencing Experiments: What Is Differential Expression?
Student 9.6 years ago, asked a question with at least 3 up-votes. For In Deep Sequencing Experiments: What Is Differential Expression?
Popular Question 9.6 years ago, created a question with more than 1,000 views. For In Deep Sequencing Experiments: What Is Differential Expression?
Appreciated 9.6 years ago, created a post with more than 5 votes. For In Deep Sequencing Experiments: What Is Differential Expression?
Popular Question 9.8 years ago, created a question with more than 1,000 views. For How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?
Good Question 9.8 years ago, asked a question that was upvoted at least 5 times. For How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?
Student 9.8 years ago, asked a question with at least 3 up-votes. For How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?
Student 9.9 years ago, asked a question with at least 3 up-votes. For Best Reference For Small Rna Alignment And Annotation
Popular Question 9.9 years ago, created a question with more than 1,000 views. For Using Ngs, What Is The Best Mirna Expression Normalization Method?
Student 9.9 years ago, asked a question with at least 3 up-votes. For Using Ngs, What Is The Best Mirna Expression Normalization Method?
Appreciated 9.9 years ago, created a post with more than 5 votes. For Using Ngs, What Is The Best Mirna Expression Normalization Method?
Student 9.9 years ago, asked a question with at least 3 up-votes. For How To Deal With Multiple Hits When Performing Mirna Expression Analysis
Student 10.0 years ago, asked a question with at least 3 up-votes. For Best Bwa Parameters For Mirna Alignment
Popular Question 10.0 years ago, created a question with more than 1,000 views. For Best Bwa Parameters For Mirna Alignment
Popular Question 10.0 years ago, created a question with more than 1,000 views. For When Aligning Mirna (Micro Rna) What Reference Is Better? (Whole Genome Or Mirbase)
Appreciated 10.0 years ago, created a post with more than 5 votes. For Should Samtools Pileup Be Performed On Uniquely Mapped Reads Or All The Reads?
Great Question 10.0 years ago, created a question with more than 5,000 views. For Should Samtools Pileup Be Performed On Uniquely Mapped Reads Or All The Reads?

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