1. 2011/03/18 AJACS 8
id:mickey24
2011 3 18

2. id: mickey24 (@mickey24)
2011 3 18

3. • DBCLS RA 2009/05
•
2011 3 18

4. NGS
2011 3 18

5. • gmap
• togofarm bot
2011 3 18

6. gmap
NGS
for Sun Grid Engine
2011 3 18

7. NGS
•
• DNA
•
TopHat -
Bowtie
Cufflinks
2011 3 18

8. DBCLS
• RA NGS
• 8CPU RAM 16GB ×8
• (Sun Grid Engine)
2011 3 18

9. 24 …
1 …
! " # $ % &&& "! "" ' (
24 …
!
"
#
$
%
&&&
"!
""
'
(
( )
2011 3 18

10. Sun Grid Engine
• qsub
$ qsub [qsub ] [ ]
• qsub
•
•
•
•
2011 3 18

11. Sun Grid Engine NGS
…
•
•
•
2011 3 18

12. $ qsub submit_tophat_job.sh [ ] /path/to/genome/mouse
/path/to/SRP000198/SRX000351/SRR001360.fastq
Your job 723552 ("foo") has been submitted
$ qstat -u mickey
$ less /path/to/qsub_log
( )
NG!
2011 3 18

13. vs /path/to/SRP000198/SRX000351/SRR001360.fastq
with
vs /path/to/SRP000198/SRX000351/SRR001361.fastq
with
vs /path/to/SRP000230/SRX000436/SRR002010.fastq
with
vs /path/to/SRP001050/SRX002424/SRR003361.fastq
with
• …
→
→
NG!
2011 3 18

14. …
gmap
2011 3 18

15. gmap
• NGS
• Sun Grid Engine
• RA
•
• TopHat
• Bowtie
• SOAP2
2011 3 18

16. GitHub
https://github.com/mickey24/gmap
2011 3 18

17. gmap
•
• gmap
•
•
•
•
COOL!
2011 3 18

18. #
ruby_path : /path/to/ruby
qsub_path : /path/to/qsub
tophat_path : /path/to/tophat
bowtie_path : /path/to/bowtie
( )
#
genome_config:
mouse:
genome_path : /path/to/genome/mouse/%s
chrnum : 1-19,X,Y
# (SRP)
project_config:
SRP000198:
tophat : "--solexa-quals -r 200 --mate-std-dev 50"
bowtie : "-X 250 -I 150"
soap2 : "-x 250 -m 150"
2011 3 18

19. gmap
@DBCLS
gmap
!"#$
$ gmap -t tophat -g mouse
/path/to/reads.fastq
qsub
2011 3 18

20. gmap
$ gmap -t tophat -g mouse /path/to/SRP000198/SRX000351/SRR001360.fastq
tool name : tophat
genome index : mouse
input file : /path/to/SRP000198/SRX000351/SRR001360.fastq
output dir : /path/to/result/SRP000198/SRX000351/SRR001360/tophat
project config : SRP000198
chrnum : 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y
submit jobs? (y/n)
y
Your job 723552 ("mt_1") has been submitted
Your job 723553 ("mt_2") has been submitted
Your job 723554 ("mt_3") has been submitted
...
Your job 723570 ("mt_19") has been submitted
Your job 723571 ("mt_X") has been submitted
Your job 723572 ("mt_Y") has been submitted
finish
2011 3 18

21. • gmap
• togofarm bot
2011 3 18

22. togofarm bot
Twitter bot
2011 3 18

23. NGS
• gmap …
• qstat
• …
2011 3 18

24. By the way…
2011 3 18

25. Twitter
•
…
2011 3 18

26. …
2011 3 18

27. 2011 3 18

28. Twitter bot
•
Twitter
• Twitter bot
•
•
•
•
2011 3 18

29. ……
2011 3 18

30. …
togofarm bot
2011 3 18

31. togofarm bot
• DBCLS
bot
•
protected
2011 3 18

32. togofarm bot
2011 3 18

33. togofarm bot
2011 3 18

34. togofarm bot
•
•
•
•
2011 3 18

35. $ gmap -t tophat -g mouse /path/to/reads.fastq
2011 3 18

36. 2011 3 18

37. 2011 3 18

38. 2011 3 18

39. @DBCLS
!"#"$%&'()"!(
(
Twitter
2011 3 18

40. • gmap NGS
( 24 )
• Twitter
( 24 )
• qstat
( 24 )
• bot
( 24 )
• ( 24 )
2011 3 18

41. 2011 3 18

42. g86.dbcls.jp
• DBCLS RA
Mac Pro
• RA Web
•
2011 3 18

43. body3d
• DBCLS BodyParts3D Twitter bot
• http://twitter.com/body3d
• http://g86.dbcls.jp/~body3d/
2011 3 18

44. body3d
2011 3 18

45. 2011 3 18

46. • NGS
• gmap
• NGS for Sun Grid Engine
• togofarm bot
• Twitter bot
2011 3 18

47. •
•
•
•
2011 3 18

48. •2
• @bonohu
• @chalkless
• @h_ono
•
• DBCLS
2011 3 18

49. 2011 3 18