User: nina.naitatmane

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Posts by nina.naitatmane

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CONTRA baseline ZeroDivisionError: float division by zero
... **I have this error in using baseline.py in contra :** bio-info@ANG-BIO-INF-NGS:~/Documents/Thanina/CONTRA/test_standart$ /home/bio-info/Documents/Thanina/CONTRA/CONTRA.v2.0.8/baseline.py --target annotationTumeurs_Solides.bed --files IonXpress_072_Tumeurs-solides-28-04-2017_17-02174-TT.bam Io ...
baseline contra written 3 months ago by nina.naitatmane10 • updated 10 weeks ago by WouterDeCoster21k
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CNVKIT scatter --range-list
... hello, Can anyone help me in using the cnvkit scatter command with a range-list? I tried to use it with a bed file like an argument (-l test.bed) in which each line looks like: "chr1 115252151 115252273 NRAS_ex4". that didn't work. Thank you ...
cnv written 3 months ago by nina.naitatmane10 • updated 3 months ago by Eric T.1.8k
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Comment: C: cnvkit , antitarget , cn , call cnv
... thank you, this helped me. how can interpret results, biologists on my lab are looking only for MET gen and its CNV ? thank you again ...
written 4 months ago by nina.naitatmane10
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cnvkit , antitarget , cn , call cnv
... hello, Im using CNVkit on amplicon sequencing with ion torrent. we don't have normal samples. and antitargets are not really helpfull in our situation, i have big insertion and no deletion in results . Is cnvkit still usefull? Can we use cnvkit without antitarget ? call command gives as a new eleme ...
cnv written 4 months ago by nina.naitatmane10 • updated 4 months ago by Eric T.1.8k
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Log 2 in CNV
... hello, I'd like to know why do we use log2 in Copy Number Variation détection ? How does it normalize data Thank you ...
cnv written 4 months ago by nina.naitatmane10 • updated 4 months ago by Eric T.1.8k
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CNVkit reference.cnn .cnr .cns log ratio
... hello, I'm trying to use cnvkit on ion torrent ngs data to detect CNVs. i'm not biologist at all, I have vague knowledge about CNVs, that's why i'm looking for someone who can help me to understand what is the reference.cnn file? and what are file extension .cns and .cnr? inorder in interpret the ...
cnvkit cnv written 4 months ago by nina.naitatmane10 • updated 4 months ago by Eric T.1.8k
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Comment: C: CNV detection techniques, algorithms, applications ...
... Thank you, it really helps, but I didn't understand the strategies :RD ,PEM, RC ..... If you have some article about that, I would be gratefull. Thank you ...
written 5 months ago by nina.naitatmane10
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Answer: A: CNV detection techniques, algorithms, applications ...
... Oh, Thanks a lot for your help :) ...
written 5 months ago by nina.naitatmane10

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