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WeiWei060512 / NUMTs-detection

Detecting NUMTs from WGS
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question about “-”strand and split reads #6

Open zqlns opened 1 year ago

zqlns commented 1 year ago

Dear wei,

Thank you for your sharing! I had two question during reading the code.

  1. Why ignore the antisense strand when defining f_nu(row) in the NUMTs_detection.sh script?
  2. I see that you don't use the split reads output from samblaster directly, but rather the WGS data. What is the reason for this.

Could you please let me know why. Thank you for your time. zhu

https://github.com/WeiWei060512/NUMTs-detection/blob/master/scripts/searchBreakpoint_fromblatoutputs.py elif row['strand'] == "-": pointFrom = "nu_NegStrand" https://github.com/WeiWei060512/NUMTs-detection/blob/master/scripts/NUMTs_detection.sh samtools view ${INPUT_WGS} ${REGION} >${OUTPUT}.sam