Moderator: Medhat

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Medhat8.4k
Reputation:
8,390
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Location:
Texas
Website:
http://combio.pl/
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Google Scholar Page
Last seen:
4 hours ago
Joined:
6 years, 8 months ago
Email:
m*************@gmail.com

 Computational biology PhD, 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 • 936 results • page 1 of 94 • next >
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... No, But I contacted the Maize database and they send it to me. ...
written 9 hours ago by Medhat8.4k
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Comment: C: Filtering tblastn results
... There 92% cover the 76 region. ...
written 8 days ago by Medhat8.4k
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Comment: C: Scientific Assessment of Software that Promises Reproducibility?
... There was a paper regarding that but I can not remember it now. but maybe take a look at this: [Ten Simple Rules for Reproducible Computational Research][1] [Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines][2] [Developing reproducible bioinfor ...
written 27 days ago by Medhat8.4k
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Comment: C: bedtools slop set start to -1
... Thanks, and I mentioned also why there was an error in my case (chromosome naming), the method you mentioned here better when you do not have `.genome` file. ...
written 28 days ago by Medhat8.4k
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Comment: C: bedtools slop set start to -1
... No, the issue was chromosome naming. ...
written 28 days ago by Medhat8.4k
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Comment: C: bedtools slop set strat to -1
... Version mismatch of the tool and documentation or what? ...
written 28 days ago by Medhat8.4k
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bedtools slop set start to -1
... Hi! I am using `bedtools slop` for padding bed file with 10k. `bedtool` version `bedtools v2.28.0` Command: `bedtools slop -header -i gene_annotations.bed -g genome_mainchrs.genome -b 10000 > gene_annotations_padding_10000.bed` Input ex: 1 11868 12227 ENSG00000223972 ..... 1 ...
gtf bed slop bedtools written 28 days ago by Medhat8.4k • updated 28 days ago by Alex Reynolds28k
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Comment: C: Having trouble with samtools cat
... Are you sure that there is `-b` option? ...
written 4 weeks ago by Medhat8.4k
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Comment: C: Converting MAF to Fasta
... OK, let your maf file called `myfile.maf` and we want the output fatsa file to be `myfile.fasta ` Then we use this command: `./maf2fasta.pl < myfile.maf > myfile .fasta` Similar question: https://www.biostars.org/p/355148/ ...
written 4 weeks ago by Medhat8.4k
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Comment: C: rename samples in a vcf or plink file
... https://www.biostars.org/p/279195/ ...
written 5 weeks ago by Medhat8.4k

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