Moderator: Medhat

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Medhat7.7k
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http://combio.pl/
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 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 • 865 results • page 1 of 87 • next >
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Comment: C: Retrieve title name by accession R vs Python
... because I am In R I used the following (feel free to advice me with something better): handel <- entrez_fetch(db = "nucleotide", id = "NC_001479.1", rettype = "gb") x -> read.xml(handle) xml_text(xml_find_all(x, "//GBSeq_organism")) The output will be: [1] "Encephalomyocarditis v ...
written 2 days ago by Medhat7.7k
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Comment: C: Retrieve title name by accession R vs Python
... unfortunately, it did not fix the main issue: using > handel <- entrez_fetch(db = "nucleotide", id = "NC_001479.1", rettype = "xml") gives empty list using > handel <- entrez_fetch(db = "nucleotide", id = "NC_001479.1", rettype = "gb") give a bulk string that is not easy to ...
written 2 days ago by Medhat7.7k
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Comment: C: Retrieve organism name by accession R vs Python
... Thanks I will try to apply that on Python or R ...
written 3 days ago by Medhat7.7k
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Comment: C: Retrieve organism name by accession R vs Python
... Not yet, I still need to find out how to extract the name from the result, or maybe there is a better solution than the one I wrote. ...
written 3 days ago by Medhat7.7k
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Retrieve title name by accession R vs Python
... I was working with R trying to get organism name (description): > handel <- entrez_fetch(db = "nucleotide", id = "NC_001479.1", rettype = "xml") # used also entre_search With fetch I get empty list with search I get an ID When I use Python. handle = Entrez.efetch(db="nucleotid ...
R entrez python written 3 days ago by Medhat7.7k
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Comment: C: best practices to use GATK with PacBio
... The question was around 3 years ago, there are tools now available for LR. This is an example: https://github.com/aquaskyline/Clairvoyante . Thanks for suggestion ...
written 3 days ago by Medhat7.7k
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Comment: C: Structural Bioinformatics - how popular
... As your question can't be answered precisely. This is a nice article (a little bit old 2016), but it may answer your inquiry especially related and external links in the article. [Spotlight on Bioinformatics][1] [1]: https://www.nature.com/naturejobs/science/articles/10.1038/nj0478 ...
written 4 days ago by Medhat7.7k
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Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
... Is the tool compares Bam to fasta/q ? ...
written 9 days ago by Medhat7.7k
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Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
... Maybe you can convert from bam to fastq `bedtools bamtofastq` and compare the result with the fastq file using ` comm -12` you have that will gave you the reads that exists in both files. Count them and compare the number with each file that will gave you an idea If they are the same. [1]: https ...
written 9 days ago by Medhat7.7k
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Comment: C: bcftools filtering error
... What is the error? can you add it to the question ? ...
written 5 weeks ago by Medhat7.7k

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