[mira_talk] Re: MIRA 3.2.1 VERSION MiraSearchESTSNPs not working

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sun, 13 Feb 2011 14:38:41 +0100

On Sunday 13 February 2011 14:21:31 walter kiprotich wrote:
>   I am experiencing problems with assembling and SNPs search (ver:
> mira_3.2.1_linux-gnu_x86_64) I use miraSearchESTSNPs pipeline to assemble
> 454 reads, 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)
> - 244 SNP
> positions tagged.Transfering reads to readpool.
> Done...................
> Saving SNP list to file: step3_d_info/step3_info_snplist.txt   What is the
> problem with my miraSearchESTSNPs pipeline. All my input files are okey
> and steps 1&2 are perfect with all files having results walter kosgei

The snplist file is for other uses: when mapping or assembling with data which 
has GenBank annotation attached. Your data obviously has not.

However, what you are searching for is in the 

file. Search for SROc, SAOc and SIOc tags. MCVc might also apply if not at the 
start or end of a contig.


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