User: Medhat

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Medhat7.5k
Reputation:
7,510
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Location:
Poland
Website:
http://combio.pl/
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Google Scholar Page
Last seen:
10 hours ago
Joined:
5 years, 5 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 • 834 results • page 1 of 84 • next >
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Comment: C: Mapping with Fasta vs fastq
... Yes I told you that in the comment above :) ...
written 2 days ago by Medhat7.5k
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Comment: C: Mapping with Fasta vs fastq
... In case of fastq: `bowtie [options]* {-1 -2 | --12 | --interleaved | } []` should not `-1 -2 or --12` used before /Users/Whole.clipped.fastq In case of fasta: > -f The query input files (specified either as m1 and m2, or as s) are FASTA files (usually having extension .fa, .mfa ...
written 3 days ago by Medhat7.5k
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Comment: C: 5 FAsta file input and showing result using nested loop
... Nice questions. Do you need the people here to answer them instead of you? You could get help If you tried something first. Try to answer them and show what you did, then sure people will help you :). https://www.biostars.org/p/75548/ ...
written 4 days ago by Medhat7.5k
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Comment: C: Tools for metagenomics classification using long reads
... Do not forget that long read comes with high error rate (15% for PacBio as example). ...
written 7 days ago by Medhat7.5k
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Comment: C: Tools for metagenomics classification using long reads
... It is not free, and the result is more general than Centrifuge. ...
written 7 days ago by Medhat7.5k
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Comment: C: Tools for metagenomics classification using long reads
... Kraken supports short read as far as I can tell, beside that Centrifuge is faster ...
written 7 days ago by Medhat7.5k
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Tools for metagenomics classification using long reads
... Searching for taxonomic sequence classifier tools that assigns taxonomic labels to reads, where the input is long reads (PacBio, ONT .....). There is already tool that could work with long read (`centrifuge`). But I would like to know if there are any other tools beside centrifuge? Thanks ...
metagenomics alignment sequen written 7 days ago by Medhat7.5k • updated 7 days ago by WouterDeCoster27k
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Comment: C: How to call CNV(copy number variant) in Pacbio ?
... You can count both as CNV ...
written 14 days ago by Medhat7.5k
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Comment: C: How to call CNV(copy number variant) in Pacbio ?
... CPV is type of SV specially deletion or duplication which both identified by Sniffles . Their is exact thread for what you asked (specially that you used sniffles ): [How to group CNV](https://github.com/fritzsedlazeck/Sniffles/issues/43) ...
written 14 days ago by Medhat7.5k
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bcftools isec window option
... Hi, In vcf-isec there is option -w : > -w, --win In repetitive sequences, the same indel can be called at different positions. Consider\n", " records this far apart as matching (be it a SNP or an indel).\n", Is there any equivalen ...
vcf sequencing written 20 days ago by Medhat7.5k

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