Moderator: Medhat

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Medhat8.9k
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8,870
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Location:
Texas
Website:
http://combio.pl/
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Google Scholar Page
Last seen:
40 minutes ago
Joined:
8 years, 3 months ago
Email:
m*************@gmail.com

 Computational biology Ph.D., 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 • 981 results • page 1 of 99 • next >
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Comment: C: how to use unix tools to convert VCF genotypes like '1|1' to this '2'
... How is your output look like? I think you should have two for loops, the first loops the samples, and for each sample loop the GT ...
written 9 days ago by Medhat8.9k
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Comment: C: Structural variations intersection
... Can you post your command? In Survivor merge there is a distance param, based on which two SVs could be counted as one. ...
written 10 days ago by Medhat8.9k
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Comment: C: Problem using PicardTools MarkDuplicates: SortingCollection: There is not enough
... You can increase memory like `java -Xms10G -Xmx20G -jar /path/to/picard-tools/picard.jar MarkDuplicates`. min: 10 max: 20 ...
written 10 days ago by Medhat8.9k
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Comment: C: Extracting the Best sequence per genomic region in a genome based on the Best e-
... Yes, we can do so: `sort -k 11,11 -g test.tsv | awk 'function abs(v) {return v < 0 ? -v : v}; {if (abs($10-$9) >= 500) {print}}'` I am using 500bp because of the difference between s. start s. end on average is 800, but you can change it as you want. If we used **800**bp the results from your ...
written 15 days ago by Medhat8.9k
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Answer: C: Extracting the Best sequence per genomic region in a genome based on the Best e-
... Did you try to use the shell command `sort -g`. For your file it will be `sort -k 11,11 -g yourFile.txt | sort -u -k2,2` ...
written 16 days ago by Medhat8.9k
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Comment: C: fastqc report and quality check
... I changed that to a comment, because it is not an answer, and we can not see the image you uploaded, refer to https://www.biostars.org/u/18713/ comment. ...
written 16 days ago by Medhat8.9k
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Comment: C: Pacific Bio Long Reads vs Illumina Short Reads
... It is a cost-effective way to detect SVs, but comes with these limitations: - low accuracy breakpoint resolution - no sequence for identified insertions - You may miss identifying short SVs (it is more suited for very large SVs) - there is a shortage of opensource tools to analyze it ...
written 18 days ago by Medhat8.9k
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Comment: C: Pacific Bio Long Reads vs Illumina Short Reads
... Based on experience and working on both. Disclaimer: This is my own paper: [Structural variant calling: the long and the short of it][1] [1]: https://pubmed.ncbi.nlm.nih.gov/31747936/ ...
written 20 days ago by Medhat8.9k
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Comment: C: Mappability file for hg38
... My bad. I thought they should follow the same structure. ...
written 4 weeks ago by Medhat8.9k
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Mappability file for hg38
... Dear All, I'm trying to download wgEncodeCrgMapabilityAlign100mer.bigWig for human genome 38. I can get the same file for hg19 from the golden path `ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/` I can not find such a file in the hg28 directory `ftp://hgdownload. ...
sequence mappabilit written 4 weeks ago by Medhat8.9k

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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?
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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?
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