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BenvenLab / eSNPKaryotyping

Analysis of Chromosomal Aberrations from RNA-Seq sequencing data.
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sh: samtools: command not found #1

Open amab424 opened 7 years ago

amab424 commented 7 years ago

Hi I get the error "sh: samtools: command not found" when I try the function 'DeletionTable'. samtools is installed in my unix environment but I'm not sure how to tell R it's there.

Thank you

BenvenLab commented 7 years ago

Hi does the samtools you have in your system is in the PATH of your linux? I mean, can you ran samtools from any directory?

Uri

amab424 commented 7 years ago

Thanks Uri. I fixed it. I just needed to use 'module load samtools' then it worked. I have another question: how do you decide the best number for the 'window' option when you use the functions 'PlotGenome' and 'Plot_Zygosity_Blocks'.

Thanks

BenvenLab commented 7 years ago

Hi you can just play with it... usually,for the PlotGenome function I use a window of 101-201, and for the Plot_Zygosity_Blocks a window of 1500000bp. However it is really dependent on the quality and depth of your sequencing. we used this values because we found that experimentally, at least for us, this gave the best result with minimal noise, but it may differ for one dataset to the other

Uri

amab424 commented 7 years ago

Hi Uri, does this tool also detect deletions? in other words, when you see a peak (high allelic ratio) does always mean amplifications? or it can mean deletions sometimes?

Thanks