Dinh/Dinh 2013/NOTES/2013-10-7: Difference between revisions

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>Dinh
(Created page with "= MEGAN analysis of unmapped reads= * I mapped the first 1000 unmappable reads with blastn $blastn -p blastn -d $dbfile -K 100 -E 100 -g F -F "m D" -a 16 -W 7 -i tmp.fa -o ...")
 
>Dinh
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* I mapped the first 1000 unmappable reads with blastn
* I mapped the first 1000 unmappable reads with blastn
   $blastn -p blastn -d $dbfile -K 100 -E 100 -g F -F "m D" -a 16 -W 7 -i tmp.fa -o $f.bwa.R1.blast
   $blastn -p blastn -d nt -K 100 -E 100 -g F -F "m D" -a 16 -W 7 -i Indx12.fa -o Indx12.bwa.R1.blast
* Result from MEGAN:
* Result from MEGAN (Indx12, Indx13, Indx14 only):
   [[File:Indx12.bwa.R1.megan.png]]
   [[File:Indx12.bwa.R1.megan.png]]
   [[File:Indx13.bwa.R1.megan.png]]
   [[File:Indx13.bwa.R1.megan.png]]
   [[File:Indx14.bwa.R1.megan.png]]
   [[File:Indx14.bwa.R1.megan.png]]

Revision as of 22:54, 7 October 2013

MEGAN analysis of unmapped reads

  • I mapped the first 1000 unmappable reads with blastn
 $blastn -p blastn -d nt -K 100 -E 100 -g F -F "m D" -a 16 -W 7 -i Indx12.fa -o Indx12.bwa.R1.blast
  • Result from MEGAN (Indx12, Indx13, Indx14 only):
 File:Indx12.bwa.R1.megan.png
 File:Indx13.bwa.R1.megan.png
 File:Indx14.bwa.R1.megan.png