Moderator: Medhat

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Medhat8.0k
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Location:
Poland
Website:
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 • 902 results • page 1 of 91 • next >
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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 5 days ago by Medhat8.0k
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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 5 days ago by Medhat8.0k
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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 5 days ago by Medhat8.0k
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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 7 days ago by Medhat8.0k
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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 8 days ago by Medhat8.0k
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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 8 days ago by Medhat8.0k
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Comment: C: pysam difference between template_length and reference_length
... Yes Tlen is template_length. > tlen deprecated, use template_length instead No reads are not spliced ...
written 9 days ago by Medhat8.0k
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Comment: C: pysam difference between template_length and reference_length
... Both `tlen` and `isize` deprecated now using `template_length` . but this have no relation with `reference_length` which is equals to `reference_end - reference_start` ...
written 9 days ago by Medhat8.0k
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Comment: C: pysam difference between template_length and reference_length
... 26S18M6D104M 6 128 57M4I75M4D12M 6 148 148M 920 148 36M1I111M 920 147 148M 151 148 148M 151 148 74M74S 74 74 148M 925 148 Actually I see both, some times template shorter sometimes the other way around. ...
written 9 days ago by Medhat8.0k
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pysam difference between template_length and reference_length
... I was trying to identify the insert size between paired reads. When using pysam `template_length` will do the work, I was confused with `reference_length` > aligned length of the read on the reference genome. This is equal to > aend - pos. Returns None if not available. I thought that ei ...
genome next-gen pysam written 9 days ago by Medhat8.0k • updated 8 days ago by Devon Ryan86k

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