Moderator: Medhat

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Medhat8.1k
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Texas
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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 • 906 results • page 1 of 91 • next >
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Comment: C: RNA-Seq data analysis mapping to closest genome as reference genome
... Is it possible that you can assemble the transcript? ...
written 20 days ago by Medhat8.1k
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Comment: C: Different output fields from efetch
... As I stated I know that the Organism name exists when using `eftech` from command line, but try the code I suggested in python it will give you only the result you get from running: `wget -O - -q "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=docsum&retm ...
written 6 weeks ago by Medhat8.1k
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Different output fields from efetch
... If I tried to get organism name using efetch like: `efetch -db nuccore -id "NC_001422.1" -format docsum | xtract -pattern DocumentSummary -element Organism` result will be: `Escherichia virus phiX174` While If I used : `handle = Entrez.efetch(db="nuccore", id="NC_001422.1", rettype="docsum")` T ...
python efetch sequence written 6 weeks ago by Medhat8.1k • updated 6 weeks ago by Pierre Lindenbaum116k
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Comment: C: Creating workflows with snakemake and conda
... Snakemake actually works on clusters and submit parallel jobs. > Snakemake can make use of cluster engines that support shell scripts > and have access to a common filesystem, (e.g. the Sun Grid Engine). In > this case, Snakemake simply needs to be given a submit command that > accepts ...
written 7 weeks ago by Medhat8.1k
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Comment: C: Using snakemake with multiple output for calling SNP using clairvoyante
... Aha, now I understand, thanks that makes more sense for me now. ...
written 10 weeks ago by Medhat8.1k
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Comment: C: Using snakemake with multiple output for calling SNP using clairvoyante
... Thanks, I will try your answer. Regarding the question I was doubting where to put it, but I thought it may fit here more. ...
written 10 weeks ago by Medhat8.1k
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Using snakemake with multiple output for calling SNP using clairvoyante
... I am trying to run Clairvoyante using snakemake for multiple chromosome. the script looks like this: chr_list = ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'c ...
snakemake snp written 10 weeks ago by Medhat8.1k
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Comment: C: Automating a SNP calling workflow
... I think you should run what you wrote and put the result/errors here besides the code, so people can help. But first; You are here overwrite the variable fq fq=~/home/administrator/Tilling-by-seq/${base}.3L_F.fastq fq=~/home/administrator/Tilling-by-seq/${base}.3L_R.fastq same he ...
written 10 weeks ago by Medhat8.1k
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Comment: C: pysam difference between template_length and reference_length
... Thanks for the information, but that will lead to this question, What is a meaning insert size? shall I add `query_alignment_length` to the equation? what is the right way to calculate it? ...
written 11 weeks ago by Medhat8.1k
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Comment: C: pysam difference between template_length and reference_length
... Thanks, It is clear now. Same topic but different issue, So If I want to calculate the insert size to be aligner independent; It will be something like: `read.next_reference_start - read.reference_end` ? "assuming that the reads aligned in the right direction" ...
written 11 weeks ago by Medhat8.1k

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