User: Medhat

gravatar for Medhat
Medhat5.9k
Reputation:
5,880
Status:
Trusted
Location:
Poland
Website:
http://comgen.pl/
Scholar ID:
Google Scholar Page
Last seen:
2 minutes ago
Joined:
4 years, 1 month 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 virus evolution and mutations, phylogeny and reverse vaccines Where others say “that’s impossible”,I say “when do I start?” (usually after a cup of coffee).

Posts by Medhat

<prev • 601 results • page 1 of 61 • next >
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Comment: C: Run a Python program in Ubuntu
... from the documentation line 21 is ``` from . import get_version __version__ = get_version() ``` you have the error because > Means you attempt to use relative import in the module which is not package http://stackoverflow.com/a/4351737/1798298 you are missing some packages I think your in ...
written 5 hours ago by Medhat5.9k
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Comment: C: Run a Python program in Ubuntu
... can you please do this ``` sed -n '20,22p' GTF_extractt.py ``` and write down the result ...
written 5 hours ago by Medhat5.9k
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Comment: C: Run a Python program in Ubuntu
... first how did you tried to run them? in general to run python script you issue command like ``` python your_script.py ``` and to know which python running the command you should run ``` which python ``` ...
written 6 hours ago by Medhat5.9k
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Comment: C: Snps annotation using snpEff or R
... I answered question like this here https://www.biostars.org/p/231960/#231963 ...
written 9 hours ago by Medhat5.9k
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Split VCF file
... I downloaded HapMap vcf file for one chromosome the file size is 11 Giga I am trying to use LiftoverVcf from Picard package, but it run out of memory. I am thinking to split the 11 giga file into smaller files each is one giga any tool can do that? or is there a better Idea? already used ``` -Xmx2 ...
vcf sequencing written 23 hours ago by Medhat5.9k
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Comment: C: ABYSS can not handel my project on 32G RAM
... I think you can run 10 normally ...
written 1 day ago by Medhat5.9k
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Comment: C: ABYSS can not handel my project on 32G RAM
... >n: minimum number of pairs required for building contigs not related to core usage ...
written 1 day ago by Medhat5.9k
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Comment: C: ABYSS can not handel my project on 32G RAM
... add this as comment not an answer; as you are using >ABYSS-P: parallel (MPI) de Bruijn graph assembler >The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single ma ...
written 1 day ago by Medhat5.9k
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Comment: C: ABYSS can not handel my project on 32G RAM
... can you support any log data about at which phase was the software running? and yes mate pairs or other long reads like SMRT PacBio or nanopore will give you better results ...
written 1 day ago by Medhat5.9k
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Comment: C: Error executing bedops convert2bed
... can you try it like this ``` cat your.vcf | /home/bedops/bin/convert2bed -i vcf - > my.bed ``` regarding memory you can use -m but as the help says it is only for sorting the bed output. > --max-mem= (-m ) Sets aside memory for sorting BED output. For example, can be 8G, 8000M ...
written 1 day ago by Medhat5.9k

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