User: Palani Kannan

gravatar for Palani Kannan
Reputation:
60
Status:
New User
Location:
Cologne, Germany
Last seen:
2 years, 11 months ago
Joined:
8 years ago
Email:
k************@gmail.com

Bioinformatics scientist

Posts by Palani Kannan

<prev • 12 results • page 1 of 2 • next >
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Allele frequencies sorted IGV visualisation
... Hi All, When I am visualising a BAM file in IGV, the reads are visible as per the mapping. I would like to visualise all mapped reads in the ascending order of alt alleles from low frequency. It is hard to scroll down and visualise 1% alt allele in 30000 reads. Thanks ...
allele frequency igv af sort written 3.2 years ago by Palani Kannan60
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Comment: C: GA4GH hap.py understanding
... I have tried all those mentioned options. I couldn't solve the issue. I moved out of GA4GH to another tool for its complexity. Thanks for your suggestion. ...
written 3.2 years ago by Palani Kannan60
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GA4GH hap.py understanding
... I am using the tool "hap.py" from GA4GH for comparing variant callers (vcf files) and following the documentation "https://github.com/Illumina/hap.py/blob/master/doc/happy.md#happy-users-manual". But, TRUTH.TOTAL get differ in each comparison cases. As truth variants are stable across all compariso ...
ga4gh hap.py documentation written 3.2 years ago by Palani Kannan60 • updated 3.2 years ago by Len Trigg1.4k
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Comment: C: Bwa Seed Length
... How do we decide "long enough" seed length? Any idea or reference? ...
written 4.0 years ago by Palani Kannan60
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Mitochondria standard for variant calling validation
... Is there any standard mitochondrial DNA sample (True positive) available to validate variant calling tools? I have seen SRM 2394, but it is having only one variants with different VAF. ...
mitochondria variant caller validation written 4.1 years ago by Palani Kannan60
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NextGene condensation alternative?
... I am bit curious about the novel condensation tool in NextGene from 2009. As it is being long years, there are any open source ideas/tools available and equivalent to the approach of the condensation tool? Specially for condensing short reads into long reads to reduce the error rate in low frequenc ...
mtdna high coverage written 4.1 years ago by Palani Kannan60 • updated 4.0 years ago by Biostar ♦♦ 20
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Answer: A: How To Filter Blast Results
... "The "Search for short, nearly exact matches" nucleotide and protein pages no longer exist. Instead, the nucleotide and protein blast programs automatically check for short queries and adjust the search parameters accordingly. This adjustment occurs when the query, either nucleotide or amino acid, i ...
written 7.8 years ago by Palani Kannan60
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Comment: C: Linux Distros Best Suited For Bioinformatics?
... I would recommend to stay with the recent and frequent updates and upgrades of Ubuntu. ...
written 8.1 years ago by Palani Kannan60
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Answer: A: Picking A Programming Language And Where To Begin
... I am also a bioinformatic programmer who started with Perl language. Currently I am using Ruby. It was created with the inspiration of perl. Currently, I am working with genome data. In terms of processing bulk data, Ruby is better in terms of memory management. I tried three different programmin ...
written 8.1 years ago by Palani Kannan60
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Comment: C: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
... Fantastic... Thanks lot :) ...
written 8.1 years ago by Palani Kannan60

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc

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