[mira_talk] miraSearchESTSNPs
- From: hegemon78@xxxxxxxxxxxxxx
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 27 May 2009 22:32:38 +0200
Hi there,
I have some problems with assembling and SNPs (ver:
mira_2.9.45_dev_linux-gnu_x86_64)
I use miraSearchESTSNPs pipeline to assemble 454 reads (with 2 strains),
but the step3_info_snplist.txt file does not contain any SNPs even
though i can find in log file for example:
...
Found
- 0 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 94 SNP
positions tagged.Transfering reads to readpool.
Done.
Storing contig ... Searching for SNPs and IUPACs, preparing needed data
... done.
Starting search:
Transfering tags to readpool.
done.
......
and close to end of file:
Saving SNP list to file: step3_d_info/step3_info_snplist.txt
any help, shall I set some switch for that?
btw.
1. I think in this pipeline, program is parsing parameter file without
problem only in 1 step (file: me_step1.par), in 2 & 3 step isn't (no
effect in results, and marks in log files).
2. Is there any way to force program to do outputs in GAP4 format for
step 1 and step 2?
Greetings,
michal
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
