View Single Post
Old 04-24-2012, 11:21 PM   #1
yksikaksi
Member
 
Location: Scandinavia

Join Date: Dec 2009
Posts: 20
Question How can I parse these reads

Code:
::::::::::::::
0H.ptFlagstat.txt
::::::::::::::
49080460 + 0 in total 
0 + 0 duplicates
6444347 + 0 mapped (13.13%:nan%)
49080460 + 0 paired in sequencing
45547041 + 0 read1  
3533419 + 0 read2   
5822436 + 0 properly paired (11.86%:nan%)  ***
5822436 + 0 with itself and mate mapped
621911 + 0 singletons (1.27%:nan%)
Good day.

I would like to parse the paired reads (***) from PCR duplicates removed sorted BAM files. I knew SAMtools or Picard tools can do that, however, I'm not sure what function or what option I should use.

Could anyone kindly please contribute the idea(s) or command line(s) or advice?

Thank you very much.
yksikaksi is offline   Reply With Quote