User: Medhat

gravatar for Medhat
Medhat6.7k
Reputation:
6,700
Status:
Trusted
Location:
Poland
Website:
http://combio.pl/
Scholar ID:
Google Scholar Page
Last seen:
1 day, 15 hours ago
Joined:
4 years, 8 months ago
Email:
m*************@gmail.com

 Computational biology PhD student, 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 • 713 results • page 1 of 72 • next >
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vcf-compare Error "Use of uninitialized value"
... I am using vcf command like this: (note: vcf file contains structure variations only ) vcf-compare -p a.vcf.gz b.vcf.gz both files are processd as follow vcf-sort -> bgzip -> tabix I got this error Use of uninitialized value $out in print at /usr/local/bin/vcf-compare line 858. ...
vcf vcf-tools written 1 day ago by Medhat6.7k
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Comment: C: Is SNPeff still the standard for variant effect prediction?
... SnpEff is good also try [VEP](http://www.ensembl.org/info/docs/tools/vep/index.html) ...
written 4 days ago by Medhat6.7k
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Comment: C: How Does Bwa Report Multi-Mapped Reads
... Do you have any idea if the MAPQ will be 0 in case of multiple mapping or something else? (I read two opinions about that) ...
written 6 days ago by Medhat6.7k
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Comment: C: deepTools draw coverage for specific region
... I think this should be another question, but I would like it to be consistent with the post. Is there a way to increase the scale of the "fraction of bases sampled" axis? in the example from documentation I could figure out that 5% of sample was covered 0 time; but what if there is more! can I ...
written 6 days ago by Medhat6.7k
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deepTools draw coverage for specific region
... I am trying to plot coverage for CDS region using deeptools. from the manual there is a flag ``` --region ```, but it either takes a chromosome or region of chromosome > –region chr10 or –region chr10:456700:891000 Is there is a way to pass bed file to it like in ``` –blackListFileName, - ...
deeptools alignment bam written 7 days ago by Medhat6.7k • updated 7 days ago by Devon Ryan69k
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Comment: C: sorting out the common path in a python script with different functions
... that is why I commented > I am missing the point ...
written 13 days ago by Medhat6.7k
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Comment: C: sorting out the common path in a python script with different functions
... It is more about coherence of the form to bioinformatics, and he also gave you a good place for programming issues stack-overflow. Otherwise you could explain how this is much related to bioinformtics and people here will be more than happy to help :) ...
written 13 days ago by Medhat6.7k
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Comment: C: Yet Another Programming Language
... After releasing the Rust-Bio paper in 2016 I did not see any thing more. ...
written 13 days ago by Medhat6.7k
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Comment: C: sorting out the common path in a python script with different functions
... maybe I am missing the point of the question. first I do not know If this a bioinformatic question. But why you do not write only one function with three argument one of them is a condition based on it you decide what to do? ...
written 13 days ago by Medhat6.7k
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Comment: C: Assembling PacBio reads using a reference genome
... None of the software in the link depends on reference AFAIK. ...
written 13 days ago by Medhat6.7k

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Appreciated 22 days ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
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Scholar 4 weeks ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
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Great Question 5 weeks ago, created a question with more than 5,000 views. For What tools you use or know for PacBio Long Read error correction?
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Appreciated 4 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Scholar 4 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Popular Question 4 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 4 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 4 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Scholar 4 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Great Question 4 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 5 months ago, created a question with more than 5,000 views. For What tools you use or know for PacBio Long Read error correction?
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