User: Medhat

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Medhat6.9k
Reputation:
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Location:
Poland
Website:
http://combio.pl/
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Google Scholar Page
Last seen:
5 hours ago
Joined:
4 years, 10 months ago
Email:
m*************@gmail.com

 Computational biology PhD candidate (searching for Postdoc :) ), Software engineer. love programming using Java, Python and R. thrive on challenges and live for breakthroughs (and coffee). working on  data analysis,genome assembly and comparative analysis.  also interested in evolution and mutations and phylogenetics.  Where others say “that’s impossible”,I say “when do I start?” (usually after a cup of coffee).

Posts by Medhat

<prev • 744 results • page 1 of 75 • next >
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Comment: C: Long read-alignment + variant calling
... Late comment, because I am curious. I do not think samtools mpileup colud call structure variation right/ also do BBmap able to call SVs from long reads? ...
written 6 days ago by Medhat6.9k
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Tools to call SVs using corrected PacBio reads
... Hi, There is a lot of tools that calls SVs from PacBio subreads. My question is; If there are tools to call SVs from corrected subreads (meaning: the PacBio subreads were corrected using short reads, by tools like proovread, jabba, lordec .. etc) If not, what software shall suit this scenario? (To ...
sv pacbio sequencing written 8 days ago by Medhat6.9k
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Comment: C: Principled structural variation detection with assembled genomes or pacbio reads
... Tools that uses PacBio to identify SVs doesn't require correction. That means they should handle the high error rates in the reads (If you know any tool that uses corrected reads let me know). ...
written 9 days ago by Medhat6.9k
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Comment: C: Pull FASTQ reads and map them with a gene
... ```samtools view input.bam "Chr10:100-200" > output.bam``` This will extract the reads from bam file that are in the region 100:200 in chr10 as example (make sure to know how your chromosomes are named). But this is the reads only (not fastq) from the reads name you can write script or maybe the ...
written 20 days ago by Medhat6.9k
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Comment: C: frequency of each nucleotide at each position in sequence
... I think you are referring to calling variant ?! something like: https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq ...
written 21 days ago by Medhat6.9k
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Comment: C: military application of bioinformatics
... but even though, still will be in military orientation I think !! ...
written 22 days ago by Medhat6.9k
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Comment: C: military application of bioinformatics
... Your answer shed the light onto an important part, But what is the maximum you think he will get from a public paper?! ...
written 22 days ago by Medhat6.9k
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Answer: A: military application of bioinformatics
... Some general topics that may help [Computational and Bioinformatics Techniques for Immunology][1] [The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats][2] [Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science][3] [Bioinformatics Scal ...
written 22 days ago by Medhat6.9k
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Comment: C: Joint variant calling
... why you are not using HaplotypeCaller? > The HaplotypeCaller is a more recent and sophisticated tool than the > UnifiedGenotyper. Its ability to call SNPs is equivalent to that of > the UnifiedGenotyper, its ability to call indels is far superior, and > it is now capable of calling non- ...
written 4 weeks ago by Medhat6.9k
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Comment: C: List of species in RepeatMasker Tool (species parameter)
... you can use ``` perl queryTaxonomyDatabase.pl -species "guinea" ``` It will give you: ``` RepeatMasker Taxonomy Database Utility ====================================== Species guinea is not in the database. Here is a list of possible similar sounding substitutes: geina goumi ginaia guynia ...
written 4 weeks ago by Medhat6.9k

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Appreciated 12 weeks ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Appreciated 3 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 3 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Scholar 3 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Great Question 3 months ago, created a question with more than 5,000 views. For What tools you use or know for PacBio Long Read error correction?
Popular Question 4 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 5 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Appreciated 6 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 6 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Popular Question 6 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 6 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 6 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Scholar 7 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Great Question 7 months ago, created a question with more than 5,000 views. For What tools you use or know for PacBio Long Read error correction?
Great Question 7 months ago, created a question with more than 5,000 views. For What tools you use or know for PacBio Long Read error correction?
Prophet 7 months ago, created a post with more than 20 followers. For Will Python Take The Place Of R?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Scholar 8 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Scholar 8 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field

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