User: Medhat

gravatar for Medhat
Medhat7.1k
Reputation:
7,110
Status:
Trusted
Location:
Poland
Website:
http://combio.pl/
Scholar ID:
Google Scholar Page
Last seen:
12 hours ago
Joined:
4 years, 11 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 • 783 results • page 1 of 79 • next >
0
votes
1
answer
108
views
1
answers
Comment: C: error while using plant ensembl biomart
... Thanks a lot, worked perfectly with no complications: library(biomaRt) host="plants.ensembl.org" mysets<-listDatasets(useMart("plants_mart", host = host)) myusemart <- useDataset("zmays_eg_gene", mart = useMart("plants_mart", host = host)) resultTable <- getBM(attribute ...
written 8 days ago by Medhat7.1k
0
votes
0
answers
134
views
0
answers
Comment: C: installing bwa for linux 32 bits
... compiled version https://github.com/lh3/bwa/tree/master/bwakit > Bwakit is a self-consistent installation-free package of scripts and > precompiled binaries, providing an end-to-end solution to read > mapping. In addition to the basic mapping functionality implemented in > bwa, bwaki ...
written 9 days ago by Medhat7.1k
2
votes
1
answer
108
views
1
answer
error while using plant ensembl biomart
... Hi, I am trying to extract gene ontology term from plant ensembl biomart using the following code: from pybiomart import Server server = Server(host='http://plants.ensembl.org') #print server.list_marts() # available marts mart = server['plants_mart'] # connecting pla ...
software error gene biomart ensembl written 9 days ago by Medhat7.1k • updated 8 days ago by Emily_Ensembl13k
0
votes
0
answers
148
views
0
answers
Comment: C: slurm script for canu assembler
... Happy that this fixed your issue. what is this `scarps.fastq.gz` where did you get it from? ...
written 9 days ago by Medhat7.1k
0
votes
3
answers
144
views
3
answers
Comment: C: What is " ./.:. " in the GT output of VCF/BCF
... I would advice you to add this to the question because it is not an answer to your question. ...
written 12 days ago by Medhat7.1k
2
votes
3
answers
144
views
3
answers
Answer: A: What is " ./.:. " in the GT output of VCF/BCF
... `./.` means that there is not enough information. for sample to match the reference ( homozygous reference) it need to be `0/0` from documentation > If a call cannot be made for a sample at a given locus, ‘.’ should be > specified for each missing allele in the GT field (for example ‘ ./. ’ ...
written 12 days ago by Medhat7.1k
0
votes
1
answer
124
views
1
answers
Answer: A: Bedtools coverage not return every line in file A
... The default behavior will give you after the line of A feature >The number of features in B that overlapped (by at least one base pair) the A interval So If it is 0 (Zero) it mean it is not covered. ---------- You could use `-d` option > -d Reporting the per-base of coverage for each f ...
written 13 days ago by Medhat7.1k
0
votes
0
answers
148
views
0
answers
Comment: C: slurm script for canu assembler
... It is clear from the log that: > -- ERROR No available machine configuration can run this task. because what was detected on your grid is class0 - 32 machines with 8 cores with 62.79296875 GB memory each. class1 - 17 machines with 1 cores with 0.0009765625 GB memory each. with m ...
written 13 days ago by Medhat7.1k
0
votes
0
answers
80
views
0
answers
PBSuite spots ambiguous insertion output value
... Hi, I am using PBSuite version 15.8.24 `Honey.py spots` was used to identify structure variations. here is one line of the output showing insertion, my question is: the insertion should be in one point in the genome, so how the output contains start and end ? (does the software add the size to sat ...
sequencing written 13 days ago by Medhat7.1k
0
votes
0
answers
148
views
0
answers
Comment: C: slurm script for canu assembler
... the error output does not show much, can you add more from the error message ...
written 13 days ago by Medhat7.1k

Latest awards to Medhat

Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to search Pfam DB using list of accessions
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Appreciated 3 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Appreciated 4 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 4 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
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
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?
Popular Question 5 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 7 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Appreciated 7 months ago, created a post with more than 5 votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 7 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics
Popular Question 8 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 8 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Popular Question 8 months ago, created a question with more than 1,000 views. For Interactive Web To Learn R
Scholar 8 months ago, created an answer that has been accepted. For A: How to find research teams regarding your field
Great Question 8 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 9 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 9 months ago, created a post with more than 20 followers. For Will Python Take The Place Of R?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Big Data Approaches For Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 568 users visited in the last hour